Oh...a buddy of mine sent this to me...he knows a lot about cars and engines, but it sounded like it makes some sense to me:
"Honestly, it really sounds like water in the tank, carbs, or both. Unscrew your float bowls (I assume this is a normal carb setup) and check for water beads. What I am guessing, and this is only a guess, is that somewhere along the line you got water in your tank. As the ski runs, the water beads get smaller (imagine shaking up oily salad dressing)and get into the fuel lines, and therefore the float bowls. The same vibrations happen in the bowls, and then it gets into the motor. This also explains why it runs fine at first, because the water is beaded up really big at first, and isn't going anywhere. I assume that since it runs fine at a certain rpm, that is a harmonic resonance that is agreeable to the ski, and is keeping the water bubbles from geting into the motor.
Again, strictly a guess, but worth a shot."
Makes sense to me except the bowls.