I've been playing around with Megaman V a bit lately, but I'm stumped on this for the moment. Stages have their standard LevelData, and this includes the boss' EnemyID, which maps to the appropriate ObjectID, etc. You can swap this out for another boss, but it seems that a routine that runs quickly resets the boss data. It looks like this might have to do with ObjectID B6, which seems to tell the game how to set up the boss.
Amusingly, if you replace a boss with a normal enemy, the routine actually doesn't run at all, but this isn't too helpful.
Anyone have any idea on how this works, or any tips on how to figure it out? I've been using the FCEUX debugger, but I haven't had much luck pinning this down yet.