As for replacing the 3 main characters, set the CHARACTER Variable in OBJCTCFG to 1, 2, or 3. For adding more characters, it's quite simple to just set CHARARCTER to 4.
Levels and music can all be done in a single WAD without having to rip Music.dta. All you need to do is replace the levels, make a new MAINCFG, and then add the music.
In other words, the Wiki is your friend.