Fixed it! I guess I was doing it wrong. For reference (run these from cmd) :
fsbext.exe -d newdir -s files.dat input.fsb (in my case it was mu_campus_se.fsb)
This will dump the files into the "newdir" directory and also create a "files.dat" file
Find the mp3 you want to replace. In my case, it was "boombox_loop.mp3". Then, import that into Audacity and trim your audio so it matches the length. Then export your trimmed track as an mp3 at 96kbps, force mono.
fsbext.exe -d newdir -s files.dat -r new.fsb
Then just rename the fsb to the original one's name, drag it into the directory it originated from, and voila
That should work! Obviously back up the original in case anything goes bad!