Hmm, I'm not an expert but Level up menu crashes must have something to do with that which affects leveling up.. I'd try a new game and disable the aforementioned one by one, testing them.When I say aforementioned,I mean the mods affecting levelling and/or perks.
Also,are you using "SaveCleaner" friend ?
All the enabling and disabling of mods might cause many orphan scripts which to need to take care of,also you need to clean your plugins with TesvEdit (The AutoClean exe).
I'd try all that if I don't want unexplained crashes on my game.