When you installed the Exhaust did you get a Jet kit for the carb? Or adjust the Air filter box at all? maybe even ad a K&N.
Sounds to me like your just running lean and need more gas. Some bikes you can get away with just adjusting hte mixture screw but its best to upgrade the jets as well. You need to make the (air in, gas, and air out all equal in a way) Max performance.
1997 VT1100C HondaShadowSpirit(Daily Driver)
1978 Honda xl125(Ranch Rider)