the bouncing you are describing is known as "porpoising", not cavitation. Cavitation is the formation of air pockets in the jet that affect impeller efficiency...
Anyway, please don't be offended, but how long have you been riding stand-ups? Most newer riders complain of porpoising until they get used to the proper place to stand in the tray and how to control the nose with leverage on the pole. Does standing further forward and leaning over the pole help?
Having said that, I put a scoop grate on my '93 superjet and it helped a lot, like you describe. You could try an extended ride plate (like the Jet Dynamics concave plate that's extended 100mm), but I'd really try different stances and riding styles first if you haven't already. Other than that, I'm not sure what else you could try, since I haven't ridden a 650sx in a very long time so I can't compare the two.
A can't think of how a new prop would help the porpoising issue, but if it is stock then it definitely needs to be changed...it's aluminum, right? Those things cavitate badly and just suck in general.
