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My Waverunner engine revs but craft goes nowhere?

My waverunner (GP 1200 R) engine runs well, no hesitation or misfire, but when starting out the craft will sit for a while before it seemingly slowly engages the prop and finally gets up to full speed. It feels like a slipping clutch. Nothing caught in the prop or jet (I have broken that down completely. What is wrong or what should I look for next?
Shane West, September 2006
My 2003 XLT1200 won't go over 25 mph in the water. I've tried putting new fuel, any other suggestions?

Kim, September 2008
A few things come to mind,
your engine turns a hollow shaft that the jet pump shaft goes inside. This is the spline inside of the hollow tube attached to your engine that goes to the rear , if this tube is stripped it will slip.
with the engine off you should not be able to turn the jetpump shaft from underneath.

Also is the engine coupler that goes to the driveshaft intact? these are made from aluminum and can fail/crack ect

The other thing that you might want to check is the jet pump impeller to housing clearance, is it in specs?If the impeller and housing are worn (from sand and other debri) the clearance might be excessive and cause slow accelleration

Johnjon, October 2006