im thinking my idle is a bit high for when my bike is warmed up. when its cool it idles around 1100 to 1300 but as soon as it gets warm 100 c it idles at 2000 to 2500. is this a normal operating idle? i think it should be lower?
So likely your carbs are not jetted correctly for the change in muffler.
CCM will likely chime in here in a bit, but I would say that you need to step up the pilot jets on the carbs, maybe even the mains to get better over all performance out of the bike.