I've had similar issues with my 2000 GTX. Once I replaced all of they grey tempo hoses and changed the fuel filter and o-ring, The ski ran fine on the trailer. In the water, the ski would not go over 30 mph and would run bogging and then rev hard and pull hard, but then fall on it's face. I ordered an Ebay special carb kit (bad decision I'm thinking) and for the love of God, I can't get this joker to even start now. I can put a little premix into the cylinders and she'll fire right up momentarily.
Any ideas or should I go back to rebuilding the carbs with genuine Mikuni parts? I've already ordered the Mikuni kits with needle and seat.