I know the parts are interchangeable 35, 40, 45, and 50, but I'm not so sure the heads, cams and valves are the same. The original 35hp parts may have been superseded with the newer/higher hp parts showing in the parts books.
In any case, if you have a good running 35, I'd leave it as is and just run the hell out of it. I doubt seriously you'll see any significant increase going to the later parts. I know there's not an awful lot of difference going from 40 to 50hp for instance. 2-3 mph on a fishing boat maybe, and nothing on a pontoon.