I totally reworked this whole system. Phil's Computer Lab's 4-1 Time Machine may work for some, but it just wasn't cutting it for me. I have enough machines to just focus on small eras. So that's exactly what I did. I swapped out the K6-III 400+ with a Pentium 100MHz and lowered the RAM from 128MB to 64MB. I took out the AWE64G and replaced it with 2 cards. A Sound Blaster Pro 2 and a Sound Blaster 16. The SBP2 is for Voice and FM, and the SB16 is for MPU-401 only. Fate of Atlantis works wonderfully now with both FM and MIDI. I also used CDBeQuiet! to change my CD-ROM to 4x. Things are just working now. This machine will play perfectly the earliest game I want, which is Atlantis, to the latest game I want, Dark Forces. I'm still playing some games to make sure there is no freezing or anything funny happening, but my hopes are high!
EDIT: WOW. JUST !@!@!@@! WOW. 5mins after posting this reply, Fate of Atlantis freezes and reboots. FFS. I cannot win with this game. At this point I'm going to start swapping CD-ROM drives. That is the only thing that has remained constant other then the Motherboard.