diff --git a/Source/Core/AudioCommon/OpenALStream.cpp b/Source/Core/AudioCommon/OpenALStream.cpp
index 8faef12da2..44b0f85325 100644
--- a/Source/Core/AudioCommon/OpenALStream.cpp
+++ b/Source/Core/AudioCommon/OpenALStream.cpp
@@ -9,6 +9,7 @@
 #include "AudioCommon/OpenALStream.h"
 #include "AudioCommon/aldlist.h"
 #include "Common/Logging/Log.h"
+#include "Common/MsgHandler.h"
 #include "Common/Thread.h"
 #include "Core/ConfigManager.h"
 
diff --git a/Source/Core/AudioCommon/WaveFile.cpp b/Source/Core/AudioCommon/WaveFile.cpp
index 5634bd4157..ca37c0e2c4 100644
--- a/Source/Core/AudioCommon/WaveFile.cpp
+++ b/Source/Core/AudioCommon/WaveFile.cpp
@@ -7,6 +7,7 @@
 #include "AudioCommon/WaveFile.h"
 #include "Common/CommonTypes.h"
 #include "Common/Logging/Log.h"
+#include "Common/MsgHandler.h"
 #include "Core/ConfigManager.h"
 
 constexpr size_t WaveFileWriter::BUFFER_SIZE;
diff --git a/Source/Core/Core/ActionReplay.cpp b/Source/Core/Core/ActionReplay.cpp
index 0e9b8aff15..8a086eb8e1 100644
--- a/Source/Core/Core/ActionReplay.cpp
+++ b/Source/Core/Core/ActionReplay.cpp
@@ -31,6 +31,7 @@
 #include "Common/CommonTypes.h"
 #include "Common/IniFile.h"
 #include "Common/Logging/LogManager.h"
+#include "Common/MsgHandler.h"
 #include "Common/StringUtil.h"
 
 #include "Core/ARDecrypt.h"
diff --git a/Source/Core/Core/Boot/Boot.cpp b/Source/Core/Core/Boot/Boot.cpp
index 76ab156221..5b719f0bcb 100644
--- a/Source/Core/Core/Boot/Boot.cpp
+++ b/Source/Core/Core/Boot/Boot.cpp
@@ -10,6 +10,7 @@
 #include "Common/CommonTypes.h"
 #include "Common/FileUtil.h"
 #include "Common/MathUtil.h"
+#include "Common/MsgHandler.h"
 #include "Common/StringUtil.h"
 
 #include "Core/Boot/Boot.h"
diff --git a/Source/Core/Core/BootManager.cpp b/Source/Core/Core/BootManager.cpp
index 6324aa40f5..33c00ec892 100644
--- a/Source/Core/Core/BootManager.cpp
+++ b/Source/Core/Core/BootManager.cpp
@@ -26,7 +26,8 @@
 #include "Common/CommonTypes.h"
 #include "Common/FileUtil.h"
 #include "Common/IniFile.h"
-#include "Common/SysConf.h"
+#include "Common/Logging/Log.h"
+#include "Common/MsgHandler.h"
 #include "Core/BootManager.h"
 #include "Core/ConfigManager.h"
 #include "Core/Core.h"
@@ -35,7 +36,6 @@
 #include "Core/HW/Sram.h"
 #include "Core/HW/WiimoteReal/WiimoteReal.h"
 #include "Core/Host.h"
-#include "Core/IPC_HLE/WII_IPC_HLE_Device_usb_bt_base.h"
 #include "Core/Movie.h"
 #include "Core/NetPlayProto.h"
 #include "VideoCommon/VideoBackendBase.h"
@@ -149,9 +149,6 @@ void ConfigCache::RestoreConfig(SConfig* config)
   config->SelectedLanguage = iSelectedLanguage;
   config->iCPUCore = iCPUCore;
 
-  config->m_SYSCONF->SetData("IPL.PGS", bProgressive);
-  config->m_SYSCONF->SetData("IPL.E60", bPAL60);
-
   // Only change these back if they were actually set by game ini, since they can be changed while a
   // game is running.
   if (bSetVolume)
@@ -279,9 +276,6 @@ bool BootCore(const std::string& _rFilename)
     // Wii settings
     if (StartUp.bWii)
     {
-      // Flush possible changes to SYSCONF to file
-      SConfig::GetInstance().m_SYSCONF->Save();
-
       int source;
       for (unsigned int i = 0; i < MAX_WIIMOTES; ++i)
       {
@@ -370,19 +364,8 @@ bool BootCore(const std::string& _rFilename)
     StartUp.bPAL60 = false;
   }
 
-  SConfig::GetInstance().m_SYSCONF->SetData("IPL.PGS", StartUp.bProgressive);
-  SConfig::GetInstance().m_SYSCONF->SetData("IPL.E60", StartUp.bPAL60);
-
   if (StartUp.bWii)
-  {
-    // Disable WiiConnect24's standby mode. If it is enabled, it prevents us from receiving
-    // shutdown commands in the State Transition Manager (STM).
-    // TODO: remove this if and once Dolphin supports WC24 standby mode.
-    SConfig::GetInstance().m_SYSCONF->SetData<u8>("IPL.IDL", 0x00);
-    NOTICE_LOG(BOOT, "Disabling WC24 'standby' (shutdown to idle) to avoid hanging on shutdown");
-
-    RestoreBTInfoSection();
-  }
+    SConfig::GetInstance().SaveSettingsToSysconf();
 
   // Run the game
   // Init the core
@@ -398,10 +381,14 @@ bool BootCore(const std::string& _rFilename)
 void Stop()
 {
   Core::Stop();
+  RestoreConfig();
+}
 
-  SConfig& StartUp = SConfig::GetInstance();
-  StartUp.m_strUniqueID = "00000000";
-  config_cache.RestoreConfig(&StartUp);
+void RestoreConfig()
+{
+  SConfig::GetInstance().LoadSettingsFromSysconf();
+  SConfig::GetInstance().m_strUniqueID = "00000000";
+  config_cache.RestoreConfig(&SConfig::GetInstance());
 }
 
 }  // namespace
diff --git a/Source/Core/Core/BootManager.h b/Source/Core/Core/BootManager.h
index b74eee675a..42dd9d7b49 100644
--- a/Source/Core/Core/BootManager.h
+++ b/Source/Core/Core/BootManager.h
@@ -10,5 +10,9 @@ namespace BootManager
 {
 bool BootCore(const std::string& _rFilename);
 
+// Stop the emulation core and restore the configuration.
 void Stop();
+// Synchronise Dolphin's configuration with the SYSCONF (which may have changed during emulation),
+// and restore settings that were overriden by per-game INIs or for some other reason.
+void RestoreConfig();
 }
diff --git a/Source/Core/Core/ConfigManager.cpp b/Source/Core/Core/ConfigManager.cpp
index e49b5cbd88..589c1e1b8f 100644
--- a/Source/Core/Core/ConfigManager.cpp
+++ b/Source/Core/Core/ConfigManager.cpp
@@ -10,7 +10,10 @@
 #include "Common/CommonPaths.h"
 #include "Common/CommonTypes.h"
 #include "Common/FileUtil.h"
+#include "Common/Logging/Log.h"
+#include "Common/MsgHandler.h"
 #include "Common/StringUtil.h"
+#include "Common/SysConf.h"
 
 #include "Core/Boot/Boot.h"
 #include "Core/Boot/Boot_DOL.h"
@@ -18,6 +21,7 @@
 #include "Core/Core.h"  // for bWii
 #include "Core/FifoPlayer/FifoDataFile.h"
 #include "Core/HW/SI.h"
+#include "Core/IPC_HLE/WII_IPC_HLE_Device_usb_bt_base.h"
 #include "Core/PowerPC/PowerPC.h"
 
 #include "DiscIO/Enums.h"
@@ -25,6 +29,39 @@
 #include "DiscIO/Volume.h"
 #include "DiscIO/VolumeCreator.h"
 
+// Change from IPL.LNG value to IPL.SADR country code.
+// http://wiibrew.org/wiki/Country_Codes
+static u8 GetSADRCountryCode(DiscIO::Language language)
+{
+  switch (language)
+  {
+  case DiscIO::Language::LANGUAGE_JAPANESE:
+    return 1;  // Japan
+  case DiscIO::Language::LANGUAGE_ENGLISH:
+    return 49;  // USA
+  case DiscIO::Language::LANGUAGE_GERMAN:
+    return 78;  // Germany
+  case DiscIO::Language::LANGUAGE_FRENCH:
+    return 77;  // France
+  case DiscIO::Language::LANGUAGE_SPANISH:
+    return 105;  // Spain
+  case DiscIO::Language::LANGUAGE_ITALIAN:
+    return 83;  // Italy
+  case DiscIO::Language::LANGUAGE_DUTCH:
+    return 94;  // Netherlands
+  case DiscIO::Language::LANGUAGE_SIMPLIFIED_CHINESE:
+  case DiscIO::Language::LANGUAGE_TRADITIONAL_CHINESE:
+    return 157;  // China
+  case DiscIO::Language::LANGUAGE_KOREAN:
+    return 136;  // Korea
+  case DiscIO::Language::LANGUAGE_UNKNOWN:
+    break;
+  }
+
+  PanicAlert("Invalid language. Defaulting to Japanese.");
+  return 1;
+}
+
 SConfig* SConfig::m_Instance;
 
 SConfig::SConfig()
@@ -32,6 +69,7 @@ SConfig::SConfig()
   LoadDefaults();
   // Make sure we have log manager
   LoadSettings();
+  LoadSettingsFromSysconf();
 }
 
 void SConfig::Init()
@@ -48,7 +86,6 @@ void SConfig::Shutdown()
 SConfig::~SConfig()
 {
   SaveSettings();
-  delete m_SYSCONF;
 }
 
 void SConfig::SaveSettings()
@@ -56,7 +93,6 @@ void SConfig::SaveSettings()
   NOTICE_LOG(BOOT, "Saving settings to %s", File::GetUserPath(F_DOLPHINCONFIG_IDX).c_str());
   IniFile ini;
   ini.Load(File::GetUserPath(F_DOLPHINCONFIG_IDX));  // load first to not kill unknown stuff
-  m_SYSCONF->Reload();
 
   SaveGeneralSettings(ini);
   SaveInterfaceSettings(ini);
@@ -70,9 +106,9 @@ void SConfig::SaveSettings()
   SaveAnalyticsSettings(ini);
   SaveNetworkSettings(ini);
   SaveBluetoothPassthroughSettings(ini);
+  SaveSysconfSettings(ini);
 
   ini.Save(File::GetUserPath(F_DOLPHINCONFIG_IDX));
-  m_SYSCONF->Save();
 }
 
 namespace
@@ -334,6 +370,47 @@ void SConfig::SaveBluetoothPassthroughSettings(IniFile& ini)
   section->Set("LinkKeys", m_bt_passthrough_link_keys);
 }
 
+void SConfig::SaveSysconfSettings(IniFile& ini)
+{
+  IniFile::Section* section = ini.GetOrCreateSection("Sysconf");
+
+  section->Set("SensorBarPosition", m_sensor_bar_position);
+  section->Set("SensorBarSensitivity", m_sensor_bar_sensitivity);
+  section->Set("SpeakerVolume", m_speaker_volume);
+  section->Set("WiimoteMotor", m_wiimote_motor);
+  section->Set("WiiLanguage", m_wii_language);
+  section->Set("AspectRatio", m_wii_aspect_ratio);
+  section->Set("Screensaver", m_wii_screensaver);
+}
+
+void SConfig::SaveSettingsToSysconf()
+{
+  SysConf sysconf;
+
+  sysconf.SetData<u8>("IPL.SSV", m_wii_screensaver);
+  sysconf.SetData<u8>("IPL.LNG", m_wii_language);
+  u8 country_code = GetSADRCountryCode(static_cast<DiscIO::Language>(m_wii_language));
+  sysconf.SetArrayData("IPL.SADR", &country_code, 1);
+
+  sysconf.SetData<u8>("IPL.AR", m_wii_aspect_ratio);
+  sysconf.SetData<u8>("BT.BAR", m_sensor_bar_position);
+  sysconf.SetData<u32>("BT.SENS", m_sensor_bar_sensitivity);
+  sysconf.SetData<u8>("BT.SPKV", m_speaker_volume);
+  sysconf.SetData("BT.MOT", m_wiimote_motor);
+  sysconf.SetData("IPL.PGS", bProgressive);
+  sysconf.SetData("IPL.E60", bPAL60);
+
+  // Disable WiiConnect24's standby mode. If it is enabled, it prevents us from receiving
+  // shutdown commands in the State Transition Manager (STM).
+  // TODO: remove this if and once Dolphin supports WC24 standby mode.
+  sysconf.SetData<u8>("IPL.IDL", 0x00);
+  NOTICE_LOG(COMMON, "Disabling WC24 'standby' (shutdown to idle) to avoid hanging on shutdown");
+
+  RestoreBTInfoSection(&sysconf);
+
+  sysconf.Save();
+}
+
 void SConfig::LoadSettings()
 {
   INFO_LOG(BOOT, "Loading Settings from %s", File::GetUserPath(F_DOLPHINCONFIG_IDX).c_str());
@@ -352,8 +429,7 @@ void SConfig::LoadSettings()
   LoadNetworkSettings(ini);
   LoadAnalyticsSettings(ini);
   LoadBluetoothPassthroughSettings(ini);
-
-  m_SYSCONF = new SysConf();
+  LoadSysconfSettings(ini);
 }
 
 void SConfig::LoadGeneralSettings(IniFile& ini)
@@ -626,6 +702,34 @@ void SConfig::LoadBluetoothPassthroughSettings(IniFile& ini)
   section->Get("LinkKeys", &m_bt_passthrough_link_keys, "");
 }
 
+void SConfig::LoadSysconfSettings(IniFile& ini)
+{
+  IniFile::Section* section = ini.GetOrCreateSection("Sysconf");
+
+  section->Get("SensorBarPosition", &m_sensor_bar_position, m_sensor_bar_position);
+  section->Get("SensorBarSensitivity", &m_sensor_bar_sensitivity, m_sensor_bar_sensitivity);
+  section->Get("SpeakerVolume", &m_speaker_volume, m_speaker_volume);
+  section->Get("WiimoteMotor", &m_wiimote_motor, m_wiimote_motor);
+  section->Get("WiiLanguage", &m_wii_language, m_wii_language);
+  section->Get("AspectRatio", &m_wii_aspect_ratio, m_wii_aspect_ratio);
+  section->Get("Screensaver", &m_wii_screensaver, m_wii_screensaver);
+}
+
+void SConfig::LoadSettingsFromSysconf()
+{
+  SysConf sysconf;
+
+  m_wii_screensaver = sysconf.GetData<u8>("IPL.SSV");
+  m_wii_language = sysconf.GetData<u8>("IPL.LNG");
+  m_wii_aspect_ratio = sysconf.GetData<u8>("IPL.AR");
+  m_sensor_bar_position = sysconf.GetData<u8>("BT.BAR");
+  m_sensor_bar_sensitivity = sysconf.GetData<u32>("BT.SENS");
+  m_speaker_volume = sysconf.GetData<u8>("BT.SPKV");
+  m_wiimote_motor = sysconf.GetData<u8>("BT.MOT") != 0;
+  bProgressive = sysconf.GetData<u8>("IPL.PGS") != 0;
+  bPAL60 = sysconf.GetData<u8>("IPL.E60") != 0;
+}
+
 void SConfig::LoadDefaults()
 {
   bEnableDebugging = false;
@@ -966,7 +1070,7 @@ DiscIO::Language SConfig::GetCurrentLanguage(bool wii) const
 {
   int language_value;
   if (wii)
-    language_value = SConfig::GetInstance().m_SYSCONF->GetData<u8>("IPL.LNG");
+    language_value = SConfig::GetInstance().m_wii_language;
   else
     language_value = SConfig::GetInstance().SelectedLanguage + 1;
   DiscIO::Language language = static_cast<DiscIO::Language>(language_value);
diff --git a/Source/Core/Core/ConfigManager.h b/Source/Core/Core/ConfigManager.h
index d76cf4d83b..40c3ea95fb 100644
--- a/Source/Core/Core/ConfigManager.h
+++ b/Source/Core/Core/ConfigManager.h
@@ -10,7 +10,6 @@
 
 #include "Common/IniFile.h"
 #include "Common/NonCopyable.h"
-#include "Common/SysConf.h"
 #include "Core/HW/EXI_Device.h"
 #include "Core/HW/SI_Device.h"
 
@@ -151,6 +150,15 @@ struct SConfig : NonCopyable
   int m_bt_passthrough_vid = -1;
   std::string m_bt_passthrough_link_keys;
 
+  // SYSCONF settings
+  int m_sensor_bar_position = 0x01;
+  int m_sensor_bar_sensitivity = 0x03;
+  int m_speaker_volume = 0x58;
+  bool m_wiimote_motor = true;
+  int m_wii_language = 0x01;
+  int m_wii_aspect_ratio = 0x01;
+  int m_wii_screensaver = 0x00;
+
   // Fifo Player related settings
   bool bLoopFifoReplay = true;
 
@@ -305,14 +313,15 @@ struct SConfig : NonCopyable
   bool m_SSLDumpRootCA;
   bool m_SSLDumpPeerCert;
 
-  SysConf* m_SYSCONF;
-
   // Save settings
   void SaveSettings();
 
   // Load settings
   void LoadSettings();
 
+  void LoadSettingsFromSysconf();
+  void SaveSettingsToSysconf();
+
   // Return the permanent and somewhat globally used instance of this struct
   static SConfig& GetInstance() { return (*m_Instance); }
   static void Init();
@@ -334,6 +343,7 @@ private:
   void SaveNetworkSettings(IniFile& ini);
   void SaveAnalyticsSettings(IniFile& ini);
   void SaveBluetoothPassthroughSettings(IniFile& ini);
+  void SaveSysconfSettings(IniFile& ini);
 
   void LoadGeneralSettings(IniFile& ini);
   void LoadInterfaceSettings(IniFile& ini);
@@ -347,6 +357,7 @@ private:
   void LoadNetworkSettings(IniFile& ini);
   void LoadAnalyticsSettings(IniFile& ini);
   void LoadBluetoothPassthroughSettings(IniFile& ini);
+  void LoadSysconfSettings(IniFile& ini);
 
   static SConfig* m_Instance;
 };
diff --git a/Source/Core/Core/Core.cpp b/Source/Core/Core/Core.cpp
index c322997cad..816811d4cb 100644
--- a/Source/Core/Core/Core.cpp
+++ b/Source/Core/Core/Core.cpp
@@ -27,6 +27,7 @@
 #include "Common/Timer.h"
 
 #include "Core/Analytics.h"
+#include "Core/BootManager.h"
 #include "Core/ConfigManager.h"
 #include "Core/Core.h"
 #include "Core/CoreTiming.h"
@@ -248,8 +249,8 @@ bool Init()
   if (g_aspect_wide)
   {
     IniFile gameIni = _CoreParameter.LoadGameIni();
-    gameIni.GetOrCreateSection("Wii")->Get(
-        "Widescreen", &g_aspect_wide, !!SConfig::GetInstance().m_SYSCONF->GetData<u8>("IPL.AR"));
+    gameIni.GetOrCreateSection("Wii")->Get("Widescreen", &g_aspect_wide,
+                                           !!SConfig::GetInstance().m_wii_aspect_ratio);
   }
 
   s_window_handle = Host_GetRenderHandle();
@@ -661,9 +662,7 @@ void EmuThread()
   // Clear on screen messages that haven't expired
   OSD::ClearMessages();
 
-  // Reload sysconf file in order to see changes committed during emulation
-  if (core_parameter.bWii)
-    SConfig::GetInstance().m_SYSCONF->Reload();
+  BootManager::RestoreConfig();
 
   INFO_LOG(CONSOLE, "Stop [Video Thread]\t\t---- Shutdown complete ----");
   Movie::Shutdown();
diff --git a/Source/Core/Core/FifoPlayer/FifoRecorder.cpp b/Source/Core/Core/FifoPlayer/FifoRecorder.cpp
index 8617b8b700..eb229bafad 100644
--- a/Source/Core/Core/FifoPlayer/FifoRecorder.cpp
+++ b/Source/Core/Core/FifoPlayer/FifoRecorder.cpp
@@ -7,6 +7,7 @@
 
 #include "Core/FifoPlayer/FifoRecorder.h"
 
+#include "Common/MsgHandler.h"
 #include "Common/Thread.h"
 #include "Core/ConfigManager.h"
 #include "Core/FifoPlayer/FifoAnalyzer.h"
diff --git a/Source/Core/Core/HW/Sram.cpp b/Source/Core/Core/HW/Sram.cpp
index 21bfea91a2..04bdf5175f 100644
--- a/Source/Core/Core/HW/Sram.cpp
+++ b/Source/Core/Core/HW/Sram.cpp
@@ -5,6 +5,7 @@
 #include "Core/HW/Sram.h"
 #include "Common/CommonTypes.h"
 #include "Common/FileUtil.h"
+#include "Common/Logging/Log.h"
 #include "Core/ConfigManager.h"
 
 // english
diff --git a/Source/Core/Core/HW/WiimoteEmu/WiimoteEmu.cpp b/Source/Core/Core/HW/WiimoteEmu/WiimoteEmu.cpp
index 0992d9e11b..28d45e2393 100644
--- a/Source/Core/Core/HW/WiimoteEmu/WiimoteEmu.cpp
+++ b/Source/Core/Core/HW/WiimoteEmu/WiimoteEmu.cpp
@@ -304,7 +304,7 @@ Wiimote::Wiimote(const unsigned int index)
   m_hotkeys->AddInput(_trans("Upright Hold"), false);
 
   // TODO: This value should probably be re-read if SYSCONF gets changed
-  m_sensor_bar_on_top = SConfig::GetInstance().m_SYSCONF->GetData<u8>("BT.BAR") != 0;
+  m_sensor_bar_on_top = SConfig::GetInstance().m_sensor_bar_position != 0;
 
   // --- reset eeprom/register/values to default ---
   Reset();
diff --git a/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_usb_bt_base.cpp b/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_usb_bt_base.cpp
index 67884c7b8d..9329036ed6 100644
--- a/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_usb_bt_base.cpp
+++ b/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_usb_bt_base.cpp
@@ -11,6 +11,7 @@
 #include "Common/CommonTypes.h"
 #include "Common/FileUtil.h"
 #include "Common/Logging/Log.h"
+#include "Common/SysConf.h"
 #include "Core/ConfigManager.h"
 #include "Core/Core.h"
 #include "Core/HW/Memmap.h"
@@ -18,15 +19,14 @@
 
 constexpr u16 BT_INFO_SECTION_LENGTH = 0x460;
 
-void BackUpBTInfoSection()
+void BackUpBTInfoSection(SysConf* sysconf)
 {
   const std::string filename = File::GetUserPath(D_SESSION_WIIROOT_IDX) + DIR_SEP WII_BTDINF_BACKUP;
   if (File::Exists(filename))
     return;
   File::IOFile backup(filename, "wb");
   std::vector<u8> section(BT_INFO_SECTION_LENGTH);
-  if (!SConfig::GetInstance().m_SYSCONF->GetArrayData("BT.DINF", section.data(),
-                                                      static_cast<u16>(section.size())))
+  if (!sysconf->GetArrayData("BT.DINF", section.data(), static_cast<u16>(section.size())))
   {
     ERROR_LOG(WII_IPC_WIIMOTE, "Failed to read source BT.DINF section");
     return;
@@ -35,7 +35,7 @@ void BackUpBTInfoSection()
     ERROR_LOG(WII_IPC_WIIMOTE, "Failed to back up BT.DINF section");
 }
 
-void RestoreBTInfoSection()
+void RestoreBTInfoSection(SysConf* sysconf)
 {
   const std::string filename = File::GetUserPath(D_SESSION_WIIROOT_IDX) + DIR_SEP WII_BTDINF_BACKUP;
   if (!File::Exists(filename))
@@ -47,9 +47,7 @@ void RestoreBTInfoSection()
     ERROR_LOG(WII_IPC_WIIMOTE, "Failed to read backed up BT.DINF section");
     return;
   }
-  SConfig::GetInstance().m_SYSCONF->SetArrayData("BT.DINF", section.data(),
-                                                 static_cast<u16>(section.size()));
-  SConfig::GetInstance().m_SYSCONF->Save();
+  sysconf->SetArrayData("BT.DINF", section.data(), static_cast<u16>(section.size()));
   File::Delete(filename);
 }
 
diff --git a/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_usb_bt_base.h b/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_usb_bt_base.h
index ea28ad17b9..7a330035f7 100644
--- a/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_usb_bt_base.h
+++ b/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_usb_bt_base.h
@@ -7,8 +7,10 @@
 #include "Core/IPC_HLE/WII_IPC_HLE.h"
 #include "Core/IPC_HLE/WII_IPC_HLE_Device.h"
 
-void BackUpBTInfoSection();
-void RestoreBTInfoSection();
+class SysConf;
+
+void BackUpBTInfoSection(SysConf* sysconf);
+void RestoreBTInfoSection(SysConf* sysconf);
 
 class CWII_IPC_HLE_Device_usb_oh1_57e_305_base : public IWII_IPC_HLE_Device
 {
diff --git a/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_usb_bt_emu.cpp b/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_usb_bt_emu.cpp
index d672464cf4..dcacf8b313 100644
--- a/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_usb_bt_emu.cpp
+++ b/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_usb_bt_emu.cpp
@@ -4,6 +4,7 @@
 
 #include "Core/HW/WII_IPC.h"
 #include "Common/CommonPaths.h"
+#include "Common/SysConf.h"
 #include "Core/ConfigManager.h"
 #include "Core/Core.h"
 #include "Core/CoreTiming.h"
@@ -33,27 +34,23 @@ CWII_IPC_HLE_Device_usb_oh1_57e_305_emu::CWII_IPC_HLE_Device_usb_oh1_57e_305_emu
     u32 _DeviceID, const std::string& _rDeviceName)
     : CWII_IPC_HLE_Device_usb_oh1_57e_305_base(_DeviceID, _rDeviceName)
 {
-  SysConf* sysconf;
-  std::unique_ptr<SysConf> owned_sysconf;
+  SysConf sysconf;
   if (Core::g_want_determinism)
   {
     // See SysConf::UpdateLocation for comment about the Future.
-    owned_sysconf.reset(new SysConf());
-    sysconf = owned_sysconf.get();
-    sysconf->LoadFromFile(File::GetUserPath(D_SESSION_WIIROOT_IDX) +
-                          DIR_SEP WII_SYSCONF_DIR DIR_SEP WII_SYSCONF);
+    sysconf.LoadFromFile(File::GetUserPath(D_SESSION_WIIROOT_IDX) +
+                         DIR_SEP WII_SYSCONF_DIR DIR_SEP WII_SYSCONF);
   }
   else
   {
-    sysconf = SConfig::GetInstance().m_SYSCONF;
-    BackUpBTInfoSection();
+    BackUpBTInfoSection(&sysconf);
   }
 
   // Activate only first Wiimote by default
 
   _conf_pads BT_DINF;
   SetUsbPointer(this);
-  if (!sysconf->GetArrayData("BT.DINF", (u8*)&BT_DINF, sizeof(_conf_pads)))
+  if (!sysconf.GetArrayData("BT.DINF", (u8*)&BT_DINF, sizeof(_conf_pads)))
   {
     PanicAlertT("Trying to read from invalid SYSCONF\nWiimote bt ids are not available");
   }
@@ -88,7 +85,7 @@ CWII_IPC_HLE_Device_usb_oh1_57e_305_emu::CWII_IPC_HLE_Device_usb_oh1_57e_305_emu
     BT_DINF.num_registered = MAX_BBMOTES;
     // save now so that when games load sysconf file it includes the new Wiimotes
     // and the correct order for connected Wiimotes
-    if (!sysconf->SetArrayData("BT.DINF", (u8*)&BT_DINF, sizeof(_conf_pads)) || !sysconf->Save())
+    if (!sysconf.SetArrayData("BT.DINF", (u8*)&BT_DINF, sizeof(_conf_pads)) || !sysconf.Save())
       PanicAlertT("Failed to write BT.DINF to SYSCONF");
   }
 
diff --git a/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_usb_bt_real.cpp b/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_usb_bt_real.cpp
index 27bddc8361..5d250309f6 100644
--- a/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_usb_bt_real.cpp
+++ b/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_usb_bt_real.cpp
@@ -496,7 +496,6 @@ void CWII_IPC_HLE_Device_usb_oh1_57e_305_real::SaveLinkKeys()
   if (!config_string.empty())
     config_string.pop_back();
   SConfig::GetInstance().m_bt_passthrough_link_keys = config_string;
-  SConfig::GetInstance().SaveSettings();
 }
 
 bool CWII_IPC_HLE_Device_usb_oh1_57e_305_real::OpenDevice(libusb_device* device)
diff --git a/Source/Core/Core/Movie.cpp b/Source/Core/Core/Movie.cpp
index 5dcab9d449..34bc547d53 100644
--- a/Source/Core/Core/Movie.cpp
+++ b/Source/Core/Core/Movie.cpp
@@ -1482,7 +1482,7 @@ void GetSettings()
   s_bNetPlay = NetPlay::IsNetPlayRunning();
   if (SConfig::GetInstance().bWii)
   {
-    s_language = SConfig::GetInstance().m_SYSCONF->GetData<u8>("IPL.LNG");
+    s_language = SConfig::GetInstance().m_wii_language;
   }
   else
   {
diff --git a/Source/Core/Core/NetPlayServer.cpp b/Source/Core/Core/NetPlayServer.cpp
index 0942eae2c1..1dbdd9bc96 100644
--- a/Source/Core/Core/NetPlayServer.cpp
+++ b/Source/Core/Core/NetPlayServer.cpp
@@ -10,6 +10,8 @@
 #include "Common/ENetUtil.h"
 #include "Common/FileUtil.h"
 #include "Common/IniFile.h"
+#include "Common/Logging/Log.h"
+#include "Common/MsgHandler.h"
 #include "Common/StringUtil.h"
 #include "Core/ConfigManager.h"
 #include "Core/HW/EXI_DeviceIPL.h"
diff --git a/Source/Core/Core/PowerPC/PPCAnalyst.cpp b/Source/Core/Core/PowerPC/PPCAnalyst.cpp
index 8e6df5d8ce..28949cfdd6 100644
--- a/Source/Core/Core/PowerPC/PPCAnalyst.cpp
+++ b/Source/Core/Core/PowerPC/PPCAnalyst.cpp
@@ -7,6 +7,7 @@
 #include <string>
 
 #include "Common/CommonTypes.h"
+#include "Common/Logging/Log.h"
 #include "Common/StringUtil.h"
 #include "Core/ConfigManager.h"
 #include "Core/PowerPC/JitCommon/JitCache.h"
diff --git a/Source/Core/Core/PowerPC/PPCSymbolDB.cpp b/Source/Core/Core/PowerPC/PPCSymbolDB.cpp
index ec000df036..7980f39e64 100644
--- a/Source/Core/Core/PowerPC/PPCSymbolDB.cpp
+++ b/Source/Core/Core/PowerPC/PPCSymbolDB.cpp
@@ -9,6 +9,7 @@
 #include "Common/CommonTypes.h"
 #include "Common/FileUtil.h"
 #include "Common/Logging/Log.h"
+#include "Common/MsgHandler.h"
 #include "Common/StringUtil.h"
 #include "Core/ConfigManager.h"
 #include "Core/PowerPC/PPCAnalyst.h"
diff --git a/Source/Core/DolphinWX/Config/InterfaceConfigPane.cpp b/Source/Core/DolphinWX/Config/InterfaceConfigPane.cpp
index 2927114e58..eb3912f306 100644
--- a/Source/Core/DolphinWX/Config/InterfaceConfigPane.cpp
+++ b/Source/Core/DolphinWX/Config/InterfaceConfigPane.cpp
@@ -19,6 +19,7 @@
 #include "Common/CommonPaths.h"
 #include "Common/FileSearch.h"
 #include "Common/FileUtil.h"
+#include "Common/MsgHandler.h"
 #include "Core/ConfigManager.h"
 #include "Core/HotkeyManager.h"
 #include "DolphinWX/Config/InterfaceConfigPane.h"
diff --git a/Source/Core/DolphinWX/Config/PathConfigPane.cpp b/Source/Core/DolphinWX/Config/PathConfigPane.cpp
index 08664dee29..a6e33b52f7 100644
--- a/Source/Core/DolphinWX/Config/PathConfigPane.cpp
+++ b/Source/Core/DolphinWX/Config/PathConfigPane.cpp
@@ -223,7 +223,6 @@ void PathConfigPane::OnNANDRootChanged(wxCommandEvent& event)
   File::SetUserPath(D_WIIROOT_IDX, nand_path);
   m_nand_root_dirpicker->SetPath(StrToWxStr(nand_path));
 
-  SConfig::GetInstance().m_SYSCONF->UpdateLocation();
   DiscIO::CNANDContentManager::Access().ClearCache();
 
   main_frame->UpdateWiiMenuChoice();
diff --git a/Source/Core/DolphinWX/Config/WiiConfigPane.cpp b/Source/Core/DolphinWX/Config/WiiConfigPane.cpp
index c53b5757d2..c5aca6124c 100644
--- a/Source/Core/DolphinWX/Config/WiiConfigPane.cpp
+++ b/Source/Core/DolphinWX/Config/WiiConfigPane.cpp
@@ -12,7 +12,6 @@
 #include "Core/ConfigManager.h"
 #include "Core/Core.h"
 #include "Core/IPC_HLE/WII_IPC_HLE.h"
-#include "DiscIO/Enums.h"
 #include "DolphinWX/Config/WiiConfigPane.h"
 #include "DolphinWX/DolphinSlider.h"
 #include "DolphinWX/WxUtils.h"
@@ -154,18 +153,18 @@ void WiiConfigPane::InitializeGUI()
 
 void WiiConfigPane::LoadGUIValues()
 {
-  m_screensaver_checkbox->SetValue(!!SConfig::GetInstance().m_SYSCONF->GetData<u8>("IPL.SSV"));
+  m_screensaver_checkbox->SetValue(!!SConfig::GetInstance().m_wii_screensaver);
   m_pal60_mode_checkbox->SetValue(SConfig::GetInstance().bPAL60);
-  m_aspect_ratio_choice->SetSelection(SConfig::GetInstance().m_SYSCONF->GetData<u8>("IPL.AR"));
-  m_system_language_choice->SetSelection(SConfig::GetInstance().m_SYSCONF->GetData<u8>("IPL.LNG"));
+  m_aspect_ratio_choice->SetSelection(SConfig::GetInstance().m_wii_aspect_ratio);
+  m_system_language_choice->SetSelection(SConfig::GetInstance().m_wii_language);
 
   m_sd_card_checkbox->SetValue(SConfig::GetInstance().m_WiiSDCard);
   m_connect_keyboard_checkbox->SetValue(SConfig::GetInstance().m_WiiKeyboard);
 
-  m_bt_sensor_bar_pos->SetSelection(SConfig::GetInstance().m_SYSCONF->GetData<u8>("BT.BAR"));
-  m_bt_sensor_bar_sens->SetValue(SConfig::GetInstance().m_SYSCONF->GetData<u32>("BT.SENS"));
-  m_bt_speaker_volume->SetValue(SConfig::GetInstance().m_SYSCONF->GetData<u8>("BT.SPKV"));
-  m_bt_wiimote_motor->SetValue(SConfig::GetInstance().m_SYSCONF->GetData<bool>("BT.MOT"));
+  m_bt_sensor_bar_pos->SetSelection(SConfig::GetInstance().m_sensor_bar_position);
+  m_bt_sensor_bar_sens->SetValue(SConfig::GetInstance().m_sensor_bar_sensitivity);
+  m_bt_speaker_volume->SetValue(SConfig::GetInstance().m_speaker_volume);
+  m_bt_wiimote_motor->SetValue(SConfig::GetInstance().m_wiimote_motor);
 }
 
 void WiiConfigPane::RefreshGUI()
@@ -186,13 +185,12 @@ void WiiConfigPane::RefreshGUI()
 
 void WiiConfigPane::OnScreenSaverCheckBoxChanged(wxCommandEvent& event)
 {
-  SConfig::GetInstance().m_SYSCONF->SetData("IPL.SSV", m_screensaver_checkbox->IsChecked());
+  SConfig::GetInstance().m_wii_screensaver = m_screensaver_checkbox->IsChecked();
 }
 
 void WiiConfigPane::OnPAL60CheckBoxChanged(wxCommandEvent& event)
 {
   SConfig::GetInstance().bPAL60 = m_pal60_mode_checkbox->IsChecked();
-  SConfig::GetInstance().m_SYSCONF->SetData("IPL.E60", m_pal60_mode_checkbox->IsChecked());
 }
 
 void WiiConfigPane::OnSDCardCheckBoxChanged(wxCommandEvent& event)
@@ -208,69 +206,30 @@ void WiiConfigPane::OnConnectKeyboardCheckBoxChanged(wxCommandEvent& event)
 
 void WiiConfigPane::OnSystemLanguageChoiceChanged(wxCommandEvent& event)
 {
-  DiscIO::Language wii_system_lang =
-      static_cast<DiscIO::Language>(m_system_language_choice->GetSelection());
-  SConfig::GetInstance().m_SYSCONF->SetData("IPL.LNG", wii_system_lang);
-  u8 country_code = GetSADRCountryCode(wii_system_lang);
-
-  if (!SConfig::GetInstance().m_SYSCONF->SetArrayData("IPL.SADR", &country_code, 1))
-    WxUtils::ShowErrorDialog(_("Failed to update country code in SYSCONF"));
+  SConfig::GetInstance().m_wii_language = m_system_language_choice->GetSelection();
 }
 
 void WiiConfigPane::OnAspectRatioChoiceChanged(wxCommandEvent& event)
 {
-  SConfig::GetInstance().m_SYSCONF->SetData("IPL.AR", m_aspect_ratio_choice->GetSelection());
+  SConfig::GetInstance().m_wii_aspect_ratio = m_aspect_ratio_choice->GetSelection();
 }
 
 void WiiConfigPane::OnSensorBarPosChanged(wxCommandEvent& event)
 {
-  SConfig::GetInstance().m_SYSCONF->SetData("BT.BAR", event.GetInt());
+  SConfig::GetInstance().m_sensor_bar_position = event.GetInt();
 }
 
 void WiiConfigPane::OnSensorBarSensChanged(wxCommandEvent& event)
 {
-  SConfig::GetInstance().m_SYSCONF->SetData("BT.SENS", event.GetInt());
+  SConfig::GetInstance().m_sensor_bar_sensitivity = event.GetInt();
 }
 
 void WiiConfigPane::OnSpeakerVolumeChanged(wxCommandEvent& event)
 {
-  SConfig::GetInstance().m_SYSCONF->SetData("BT.SPKV", event.GetInt());
+  SConfig::GetInstance().m_speaker_volume = event.GetInt();
 }
 
 void WiiConfigPane::OnWiimoteMotorChanged(wxCommandEvent& event)
 {
-  SConfig::GetInstance().m_SYSCONF->SetData("BT.MOT", event.GetInt());
-}
-
-// Change from IPL.LNG value to IPL.SADR country code.
-// http://wiibrew.org/wiki/Country_Codes
-u8 WiiConfigPane::GetSADRCountryCode(DiscIO::Language language)
-{
-  switch (language)
-  {
-  case DiscIO::Language::LANGUAGE_JAPANESE:
-    return 1;  // Japan
-  case DiscIO::Language::LANGUAGE_ENGLISH:
-    return 49;  // USA
-  case DiscIO::Language::LANGUAGE_GERMAN:
-    return 78;  // Germany
-  case DiscIO::Language::LANGUAGE_FRENCH:
-    return 77;  // France
-  case DiscIO::Language::LANGUAGE_SPANISH:
-    return 105;  // Spain
-  case DiscIO::Language::LANGUAGE_ITALIAN:
-    return 83;  // Italy
-  case DiscIO::Language::LANGUAGE_DUTCH:
-    return 94;  // Netherlands
-  case DiscIO::Language::LANGUAGE_SIMPLIFIED_CHINESE:
-  case DiscIO::Language::LANGUAGE_TRADITIONAL_CHINESE:
-    return 157;  // China
-  case DiscIO::Language::LANGUAGE_KOREAN:
-    return 136;  // Korea
-  case DiscIO::Language::LANGUAGE_UNKNOWN:
-    break;
-  }
-
-  PanicAlert("Invalid language. Defaulting to Japanese.");
-  return 1;
+  SConfig::GetInstance().m_wiimote_motor = event.IsChecked();
 }
diff --git a/Source/Core/DolphinWX/Config/WiiConfigPane.h b/Source/Core/DolphinWX/Config/WiiConfigPane.h
index a185751c24..beffa23f99 100644
--- a/Source/Core/DolphinWX/Config/WiiConfigPane.h
+++ b/Source/Core/DolphinWX/Config/WiiConfigPane.h
@@ -8,11 +8,6 @@
 #include <wx/panel.h>
 #include "Common/CommonTypes.h"
 
-namespace DiscIO
-{
-enum class Language;
-}
-
 class DolphinSlider;
 class wxCheckBox;
 class wxChoice;
@@ -40,8 +35,6 @@ private:
   void OnSpeakerVolumeChanged(wxCommandEvent&);
   void OnWiimoteMotorChanged(wxCommandEvent&);
 
-  static u8 GetSADRCountryCode(DiscIO::Language language);
-
   wxArrayString m_system_language_strings;
   wxArrayString m_aspect_ratio_strings;
   wxArrayString m_bt_sensor_bar_pos_strings;
diff --git a/Source/Core/DolphinWX/FrameTools.cpp b/Source/Core/DolphinWX/FrameTools.cpp
index f2c47fdb8e..502380762e 100644
--- a/Source/Core/DolphinWX/FrameTools.cpp
+++ b/Source/Core/DolphinWX/FrameTools.cpp
@@ -1180,7 +1180,7 @@ void CFrame::DoStop()
     if (NetPlayDialog::GetNetPlayClient())
       NetPlayDialog::GetNetPlayClient()->Stop();
 
-    BootManager::Stop();
+    Core::Stop();
     UpdateGUI();
   }
 }
diff --git a/Source/Core/DolphinWX/NetPlay/NetWindow.cpp b/Source/Core/DolphinWX/NetPlay/NetWindow.cpp
index 90f60e3c1b..596de8676d 100644
--- a/Source/Core/DolphinWX/NetPlay/NetWindow.cpp
+++ b/Source/Core/DolphinWX/NetPlay/NetWindow.cpp
@@ -32,6 +32,7 @@
 #include "Common/FifoQueue.h"
 #include "Common/FileUtil.h"
 #include "Common/IniFile.h"
+#include "Common/MsgHandler.h"
 
 #include "Core/ConfigManager.h"
 #include "Core/HW/EXI_Device.h"
diff --git a/Source/Core/DolphinWX/VideoConfigDiag.cpp b/Source/Core/DolphinWX/VideoConfigDiag.cpp
index 38fe322b01..b494659ca7 100644
--- a/Source/Core/DolphinWX/VideoConfigDiag.cpp
+++ b/Source/Core/DolphinWX/VideoConfigDiag.cpp
@@ -886,10 +886,6 @@ VideoConfigDiag::VideoConfigDiag(wxWindow* parent, const std::string& title)
                                         this);
 
         progressive_scan_checkbox->SetValue(SConfig::GetInstance().bProgressive);
-        // A bit strange behavior, but this needs to stay in sync with the main progressive boolean;
-        // TODO: Is this still necessary?
-        SConfig::GetInstance().m_SYSCONF->SetData("IPL.PGS", SConfig::GetInstance().bProgressive);
-
         szr_misc->Add(progressive_scan_checkbox);
       }
 
diff --git a/Source/Core/DolphinWX/VideoConfigDiag.h b/Source/Core/DolphinWX/VideoConfigDiag.h
index dcff2803e2..e02591956c 100644
--- a/Source/Core/DolphinWX/VideoConfigDiag.h
+++ b/Source/Core/DolphinWX/VideoConfigDiag.h
@@ -130,9 +130,7 @@ protected:
 
   void Event_ProgressiveScan(wxCommandEvent& ev)
   {
-    SConfig::GetInstance().m_SYSCONF->SetData("IPL.PGS", ev.GetInt());
     SConfig::GetInstance().bProgressive = ev.IsChecked();
-
     ev.Skip();
   }
 
diff --git a/Source/Core/InputCommon/InputConfig.cpp b/Source/Core/InputCommon/InputConfig.cpp
index 9df0b71e62..019ddeb414 100644
--- a/Source/Core/InputCommon/InputConfig.cpp
+++ b/Source/Core/InputCommon/InputConfig.cpp
@@ -6,6 +6,7 @@
 
 #include "Common/FileUtil.h"
 #include "Common/IniFile.h"
+#include "Common/MsgHandler.h"
 #include "Core/ConfigManager.h"
 #include "Core/HW/Wiimote.h"
 #include "InputCommon/ControllerEmu.h"
diff --git a/Source/Core/UICommon/UICommon.cpp b/Source/Core/UICommon/UICommon.cpp
index 4459ec8090..ece3d2d2ee 100644
--- a/Source/Core/UICommon/UICommon.cpp
+++ b/Source/Core/UICommon/UICommon.cpp
@@ -9,6 +9,7 @@
 #include "Common/CommonPaths.h"
 #include "Common/FileUtil.h"
 #include "Common/Logging/LogManager.h"
+#include "Common/MsgHandler.h"
 
 #include "Core/ConfigManager.h"
 #include "Core/HW/Wiimote.h"
diff --git a/Source/Core/VideoBackends/D3D/D3DBase.h b/Source/Core/VideoBackends/D3D/D3DBase.h
index 52d7b446d0..24c6848434 100644
--- a/Source/Core/VideoBackends/D3D/D3DBase.h
+++ b/Source/Core/VideoBackends/D3D/D3DBase.h
@@ -10,6 +10,7 @@
 #include <vector>
 
 #include "Common/Common.h"
+#include "Common/MsgHandler.h"
 
 namespace DX11
 {
diff --git a/Source/Core/VideoCommon/VideoConfig.cpp b/Source/Core/VideoCommon/VideoConfig.cpp
index 13da3ef47a..73e6eafa12 100644
--- a/Source/Core/VideoCommon/VideoConfig.cpp
+++ b/Source/Core/VideoCommon/VideoConfig.cpp
@@ -8,6 +8,7 @@
 #include "Common/CommonTypes.h"
 #include "Common/FileUtil.h"
 #include "Common/IniFile.h"
+#include "Common/MsgHandler.h"
 #include "Common/StringUtil.h"
 #include "Core/ConfigManager.h"
 #include "Core/Core.h"