Two issues I ran into. One is having enough conventional memory. I used EMM386 with these paramters in config.sys:

dos=high,umb
...
device=c:\util\emm386.exe ram i=b100-b7ff i=c600-c7ff i=cc00-cfff i=e600-efff frame=d000 a=32 d=128 notr

The other issue was cdrom.sys from pc 2004 vm addon which played the wrong audio tracks. I used this driver (vide-cdd.sys) instead:

http://jeffareid.net/misc/videcdd.zip

A third issue unrelated to a specific game was not being able to copy files from some .iso images, I kept getting file not file. This was solved by buring the iso image to a true cd-rom, and in some cases, copying the files, and then re-burning the cd-rom.

Here's a video of the final sequence in the game, followed by a suprisingly good ending credit song:

http://jeffareid.net/game/aitd3.wmv

Here's the song:

http://jeffareid.net/game/aitd3.mp3