New update. Had a chance to spend some time at the lake today. Here is what I have done today. Pulled the carb that goes to the 99 GS off and put it back on the proper ski. Triple checked the high and low speed screw settings on the new carb, and re-installed it on the 02 GTI LE. Also put another temp sensor on the 02, as some have suggested that there is a chance this could be the culprit. I also changed the fuel line from the Sea Doo Fuel filter (even though it looked great), and the in line fuel filter after that. I also changed out the pulse line. Is it odd that it is on the mag side? On my other skis it is on the PTO side.
All of this to say there was NO NET CHANGE. The ski behaved exactly the same as it had before. It still delays when you grab a handful of throttle. That delay does get worse the longer you ride.
This leaves me still puzzled and wondering a few things:
1. Could the rotary valve be off a degree or two and thus causing the problem?
2. I have heard of the clearance being off on the rotary valve causing bogging problems, could this be reasonable?
3. What tools will the Dealership use to try and diagnose this? Do the plug in diagnostic tools provide a great deal of information?
4. Could the engine being misaligned cause any of this? I thoroughly don't believe that this is even possible, but I find myself doubting everything that I have done thus far now.
Also had the fun realization that the front left motor mount was broken. Not as terrible to swap out with the ski in place as I thought.
One other thought, out of the water (on or off of a hose) it will rev immediately and without any hesitation whatsoever.
Ok, I suppose that's about everything. Anything else I should consider before going to the dealership? Planning to just ride it as is next weekend for Labor day, and then drop it off after that and ask them to sort it out. It is so close to being right that it is making me crazy.
Thanks in advance.