Id recommend porting the carb to 41mm. That way it you can use your stock carb and it gives good gains across the board for cheap. You would pick up around 2hp and still not have to pull motor apart to do it. That is my suggestion and I think most would agree.
I installed the kTm 540 kit, had the head ported to include the bigger valves by Moto Headz Racing, and installed the 8/06 cam, the carb is still stock. It runs very well from the bottom to the top and I ride in the dunes of SoCal. The biggest seat of the pants dyno in the world. Good luck!!!
I live up in Victorville and ride out there all of the time in the desert. This quad has alot of power stock but I can never seem to leave anything alone. I appreciate all of the input. I was thinking of having the carb bored first. I may just start there.