I have a 2000 gp1200r with a 140 hours on it.
It has a riva D-plate, Cat sensor chip, Free flow exhaust, Pro-tec moflow intake grate, Pro-tec extended ride plate, and a pump plug kit.
The cat.con. lasted until like 120 hours. Since I replaced it I have had problems in midrange with it bogging. It will idle fine, and it will run top end fine also. In the midrange it sounds like it drops a cylinder, but if you open it up it clears out and runs fine.
I did not do anything with the high/low adjustments on the carbs when I installed the D-plate. I read on this forum that was not necessary in several places. I also read that most of you hate the yamaha 2m oil. I have been using it since new. Now I read that was not a good plan. I checked the plugs several times during different days and usually one of them appear fouled, but its always different cylinders. I also have since read that my powervalves are probally filthy. From what I read, I need to pull the head, to clean them correctly. So that sounds like a good time for a performance head install. I would like to figure out my problem before doing anymore upgrades. I also read that US skis seemed to be rich from the factory. Could this be the problem coupled with the D-plate?
I would appreciate any suggestion anyone has.

just in case you weren't aware, in order to check the plugs you need to do a plug chop - ie run the ski at the rpm that is of interest for a couple minutes then pull the lanyard - then remove the spark plug while still out on the water (easier to do if you leave your seat on the dock) best if you take some extra plugs with you

so I'd suggest doing a plug chop at the problem rpm and then compare the plugs with

http://www.dansmc.com/spark_plugs/spark_plugs_catalog.html

NPR GP2,I had that exact same ski, and almost all the mods that you have, same hrs. and get this....same problem at 145 hrs. But I was wanting a 1300, so just traded it in instaed of doing a carb rebuild. And thats what I think was wrong with ski...

FL AIR has it on the nose.

130 hours... same problem.

Rebuilt the carbs... problem solved.

Rebuilt the carbs...
But no High/low speed adjustment with removing tamper proof caps?
Or just a straight carb rebuild?
And should I go with the riva flame arrestors or just leave it stock?
And what is anyones thoughts on the Stinger 3 Pipe, as opposed to stock with the d-plate?
Thanks for the help!

I would go with the flame arrestors, they really open things up. A stinger 3 will help the acceleration, any bogging (I know on mine before the stinger it had terrible bogging until about 5k RPM) was gone.