Doesn't sound like overheating to me. When a bike overheats the radiator generally boils over, it runs raspy, and you can smell the motor running hot.
I have found that if I'm off the throttle for a while, it will load up a bit; example, if I'm descending down a long hill, it may take a couple of seconds for the carb to clear out when I get back on the throttle. If I were to hammer the throttle in this situation I think it may cut out.
By the way, I have a 99' 220 with a Procircuit Pipe, air box mods, FRP porting, and stock carb. My carb is 38 pilot, 145 main, and needle on top clip (leanest) at sea level. I testing multiple jetting combos and found that a bigger pilot just created more spooge.