Much as I love the BGM included in Windom, I decided to go one step further and try to make it even more "Gundam-y", by trying to import my own tracks into the game. Before trying anything mentioned below, I strongly suggest making a backup copy of your Sound folder somewhere else on your hard drive, for reference and to repair any accidental damage done while tinkering.
As far as I can tell, if your music file is in .ogg format, placed in the Sound folder with the same name as the original sound file (i.e. fuse.ogg if you want to change the music for the first level), and *approximately the same length as the original file*, it'll work. I tried using the "Finale" track from the Gundam Seed Symphony collection because it's a fairly long and varied piece, and unedited (it's approximately 7:40 long) it didn't work. When I cut it down to 3:55 (1 second below the original length of the fuse track), and tried again, it worked fine.
I'd be interested to know if it is directly tied to the length of the file being replaced, or if you can get away with longer files (and if so, by how much).