Interesting idea. So you are using some kind of editor to create this, like the editing tools for Oblivion/Morrowind, The Witcher, and such? I would love to play this kind of class in-game.
I do agree, though, Jodan especially should have some sort of stamina loss while using it. My buddy does Jodan and he said one of the things he had to get used to was holding the shinai over his head for so long.
Also, no Nito?! You should definitely work that in later :-D.
And yes, a script to distinguish between armor would be good. Maybe something up to a "medium" type armor (not sure where that line would be drawn in this game". I can see your point for having heavy armor + all of these bonuses would make your character way Over-powered.