did you check the cushions in the clutch basket?
grab the basket infront of the gear and try and turn it back and forth... if the basket turns and the gear does not... then the cushions are shot... I had a bike I could not find a knock noise and thats what it ended up being....
as far as the tranny goes, the shift star mod, shaft mod, and easy shift spring help.... but it still does not make it great...
I have heard some people cutting every other "dog" off the tranny gears to help it shift better but I have never rode a bike with said mod....