Why does my bike backfire or pop after changing the pipes?

This is an easy fix. The popping is caused by unused fuel being dumped into the exhaust header after you close the throttle. That fuel is ignited by air injected into the headers (just past the exhaust valve) when the throttle is closed. This reduces the amount of hydrocarbon emission spewed by your bike on deceleration. The stock mufflers effectively mute the popping.

The fix is to "marble" your system or remove the air injection system completely. Details on this Fixit page.