I REALLY like this mod (more for the custom/secret boss). This is such a good idea to make the original boss harder and even add bonus/secret boss to the game, the only thing is in solo its really hard example to beat bowser 3 (maybe just skill issue, we never know i started played sm64 its been a week.)
As for the Bowser 2 fight, are you playing with friends? That particular fight is notorious for networking issues like that, even in vanilla. Let me know if you ARE playing solo, as I've rarely seen that fight break in that context.