It is probably not your TPS. Try adjusting your idle speed up first, if that doesn't help you should consider re-setting the throttle (make sure you get 0 and 100) with your Power Commander software and then maybe try adjusting the fuel % in your map at 0 and 10% throttle position and at the lower rpm ranges. If your bike was running fine before your mods it's probably not your TPS. You didn't mention whether you have a full system or just an end can, simce you did the block off plates I assume you went with the full system. I don't think it is unusual for your idle speed to drop when the bike is warm and the weather is really hot.
it's the muzzy pipe, I am always adjusting my idle to keep mine running, since I switched from the akro to the muzzy. My bike was dyno tuned wiht the pc3 and the tps has been set, throttle bodies have been synchornized, and I still have to play with the idle