I just replaced the spark plugs. One was really bad, the prong was bent all the way to the post. My prediction, it wasn't firing and the piston kept knocking it and bending it because there was no combustion to compress the piston back. Waverunner running on one piston=reduced HP which is probably why it was bogging down and shutting off. The engine wasn't powerful enough to push adequate water through the jet. I haven't put it in the water yet to see if this worked, but I will this weekend.
Chris
September 2009