That seems odd to me. Did you change the air filter as well? Anytime you increase the airflow through the engine, what a pipe and air filter will do, you need to go up in jet size. Unless the LT80s come real rich from the factory, you should need a larger jet. A plug check will tell you alot as well. (looking for a beer bottle brown color) Too white you are running lean(need larger jet), too dark, running too rich(need smaller jet). You can adjust the idle with the air mixture screw on the side of the carb (may help it run better as well).
I would call Rich at Hetrick racing 814-676-0477, or
http://www.hetrickracing.com/ he really knows his stuff and can get you dialed in perfectly. Just tell him what you have and where you ride, and he can get real close on the jetting, then it is just trying different sizes and picking which one works best.