Okay, so it turns out that the (U) version of Infernal Machine *hates* the settings that provide good audio for the (E) version. (I have no clue why I didn't notice this until now.) After a lot of dicking around, I found that AI=540 provided a usable compromise, where the sound is in synch and doesn't crackle like crazy. The problem is that the main menu music is now too fast. None of the other Factor 5 games behave this way.
In an ideal world the (U) version would be placed into a refrigerator and have a small atomic device detonated next to it. Until PJ64 gets proper audio synch or Azimer does something magical, I don't see that version working properly.
This fix isn't quite satisfactory, but with 2200\875, the last 30 seconds or so of the intro have no sound effects, only music. (A bug that could affect other FMVs throughout the game in theory.) 1500\530 has a wee bit of pop and crackle, but the FMVs now work correctly.
The Project64 recompiler is mostly to get games running at full speed for playability, but this is not a game, and implementing memory address range prediction in the recompiler to prevent missing the branch weighs would possibly not be worth it for a demo which should run fast enough with the interpreter.
With these changes, games such as RE2 now use Fixed Audio timing with appropriate VI\AI values, and now have near-perfect audio that will no longer bug out randomly, due to low framerates, or when loading save-states. Infernal Machine no longer has crackling audio. San Francisco Rush 2049 seems improved. Rogue Squadron\Naboo have fixed sound. Tarzan, Rugrats, and other games using Factor 5 tech were adjusted. Some ran fine on vanilla settings for some reason.
I disabled "Start Changed" for Naboo and Infernal Machine, since having it enabled causes significant stuttering in some menus.
FYI, MORT is the name of the speech codec used by Factor 5 games.
I decided on VI=2200 and AI=785 for most titles because those values hit a sweet spot between stopping crackle and keeping sound in synch. (Some games were happy with AI=400.) Some further tweaking might provide better results.
Changing to CF1 fixes the jeep handling and some nasty stuttering.
Disabling Fast SP fixed some crashes with recompiler. Also seems to fix environment flicker?
Plus some other tweaks.
The game seems stable on a custom build (with the Factor 5 hack) with CPU recompiler and cxd4 RSP interpreter during testing except for the end of levels, when Indy's Trading Post causes the game to crash without Interpreter. The game appears to be far more stable in PJ64 than mupen64plus, however the game's audio timings are off, and the sound crackles. But I was able to drive Indy's jeep round in circles for 15 minutes without a single lockup.
zilmar