Hey mate.
Sounds like the same symptoms I had with my xpdi. Mine turned out to be my fuel pump. Bogging out round 4000rpm. I found it hard to actually narrow it down to the fuel pump as the engine worked perfectly and fuel pressure was on specs on the trailer. As SMC mentioned, you have to tee in the fuel pressure gauge and observe fuel pressure when the ski bogs down on the water. i hooked it up before the filter.
You can also confirm if it is a fuel issue by disconnecting the fuel return line at the fuel tank and observing the amount of fuel returning to the tank from the fuel rail whilst riding. When the ski bogs out, if there is little or no fuel returning back to the tank, and fuel pressure drops you know its ya fuel pump.
There are checks in the Manual to test the air compressor output and the fuel pressure regulator too. You should get 27 +- 2 psi upon connecting the lanyard to test the fuel pressure regulator.
There are many threads on the DI fuel pumps on this forum. They helped me a lot with my machine. This thread is a good one
http://www.seadooforum.com/showthread.php?46680-DI-Seadoo-Fuel-Pump&highlight=di+fuel+pump
Good luck.