Most likely the carbon ring on the driveshaft may not be tight enough, allowing the pump to suck air from inside the hull under hard accelleration. Take the seat off, reach down inside and try to pull the front of the black rubber bellows on the driveshaft back towards the stern... if it's not VERY difficult to pull back, then it needs adjusting. Their are 2 clamps on the bellows, the forward clamp holds the carbon ring in place and the aft clamp holds the bellows in place... loosen the aft clamp, pull the bellows forward as much as you can and re-tighten the aft clamp.
A 50 hour supercharger rebuild? I've not heard of that before, everything I've read says they only require 100 hour rebuilds.
ps. Also you need to include your year and model information when posting a question in the future.
- Michael