I have not experimented with changing the loops in OP as it's not really necessary to get the effect I want. I have the rock version of the DS9 theme as my menu music, and the Feds get the TNG TV Theme, which goes into the 1st contact comm chatter, then to the standard music. You could just as easily have The Wrath of Khan music as the entire Federation in game music if you want. Make sure yout file is a wav, not mp3 as SFC3 uses, and that it is 16 bit Stereo, 22050.
If your music is a big enough file, the whole song will play. It is better to add the music to the zip and then alter SFCMusic.txt in assets\sound, at least for my purposes.
SFC1, well, I know that Cool Edit Pro tries to interpret the I4X format but it just comes out as static. Has anyone managed to convert that to wav or mp3?