Well, I use a MT-32 2nd gen, not a CM module. I assume those two are the same minus the PCM sound effects?

No, LucasArts has with "Indiana Jones and the Fate of Atlantis" the one score that most needs being worked on --- not because of the shortcomings of the MT-32, but because of the low quality of the music editing. There's tons of bad notes, unquantized stuff and bad instrument choices, like "Str Sect 3" for orchestral strings. And of course, the existing enhancement offered on some website doesn't fix that at all, it just changes the instruments and plays it on some modern synth with crappy soundfont, making it sound even worse.
(I already did the editing for my own purposes.)

You have to be aware that midi music is not simple as you think.
In the past there was no midi standard (no general midi) and all midi music for games was made for Roland MT-32 synthesizer. Later games were designed for Roland CM-32L synthesizer (appeared also as a PC card as Roland LAPC-I) which was enhanced MT-32 (had extra sound effects - gunshot, thunder, etc.). Although both modules (mt and cm) claimed to be compatible they were actually not. Games designed for cm-32l used extra sound effects not available on mt-32 and also transfered midi messages faster so that slow mt-32 couldn't handle that. Also games designed for mt-32 exploited its bugs. The bugs were removed in cm-32l so games that used them didn't sound correctly on later module. The important thing about mt and cm modules is that they were programmable - the musician could create completely new instruments with them. And they did that. That is why no other midi device is compatible with them (actually there were later roland modules: cm-64 and cm-500 that are compatible). But nothing else is. If the game music was designed for one of them there was nothing else that could play that music correctly. That music was also almost perfect. Later games were designed for Roland SCC-1 (sound canvas). This module couldn't create new instruments but still if the game was designed for it there was nothing else that could play the music correctly cause of differences in instruments and their volume - in extreme cases some instruments are not being heard at all on other sound modules cause of that. Later Roland released later models of sound canvas but still cause of slight differences between them game music only sound correctly on the model it was designed for.
All above modules were very expensive and not many people had them. At the same time there was Adlib (and later Sound Blaster) with its frequency modulation (fm) synthesis that tried to emulate instruments but the quality of most of them was very poor - and that is what most people remember. Later General MIDI specification appeared and sound cards with wavetable synthesis appeared but they obviously couldn't play games music properly cause it was designed either for mt-32 or scc-1. Later some games were designed for Gravis UltraSound and later for Sound Blaster AWE32.

The important thing here is if you want to enhance any game music you have to know how that music sounds. So you have to play that music on synthesizer it was designed for. In most cases that game music is so perfect it doesn't need any tuning as the devices were very good and expensive. Sometimes some instruments could be improved. That music was also written by payed professionals and is really perfect. Technology was really not a limitation for them. Check for example old Star Wars music. You cannot enhance it. Old games were limited with graphics: number of colors, resolution, etc. and that can be improved. You cannot add maximum reverb to every instrument cause that is not new technology enhancement. Reverb was available in the past and if it was not used there was a reason for it. Same would go for applying maximum bass in amplifier to enhance music. If the music designer wanted more bass he would use it. If you want people to play the game with good music just allow them to play the game with the music the game was designed for with some slight modifications that were not available in the past. If you are not a professional you are simply not able to make better song than professional. You cannot change instruments. Your advantage is only modern technology. Like you can add higher resolution graphics or 3d,  even adding higher resolution textures is somewhat controversial as you have to be good at it. you can add speech (ok, it won't be by professional actors but at least better than nothing), you can add touch interface, port it to mobile devices. But with music it is different as it was already perfect that time. MT-32 was 32kH stereo.

I am not a musician so also take a look at what musicians who also enhance old games music have to say:
(link to here)

What about General Midi emulation? I know it's built into Windows, but doesn't quite sound like the real thing. I used an SCC-1 back in the day.

I imagine it might be the same issue affecting the "Space Alvin" patch, described on the earlier pages of this thread. I'll try to take a deeper look sometime this week...

https://skydrive.live.com/redir?resid=81940F2FC1006A8A!223&authkey=!Uc0V5cXIiGU%24

I put up a recording of it on my side. I can hear where there are what sound like phasers on the guitar hits in the CM32L. I don't remember ever hearing those on an MT-32.

Anyone have an MT-32 *hooked up* they can use to see if it has the phaser hits as well? All I can find are CM-32L/LAPC-I recordings of this track.