How Air Injection Works
To meet federal regulations, OEM's use clean air injection that adds oxygen to the exhaust. This allows unburnt fuel to burn and reduce hydrocarbon emissions into the atmosphere. For this to properly work, stock exhaust systems have a catalytic converter inside that completes the process.
Once an aftermarket exhaust system is installed the added oxygen does little to help burn the excess fuel. Instead, it often leads to "backfiring" or "popping" when engine braking or decelerating. By disabling the clean air injection one can nearly eliminate all backfiring. Also, since the clear air injection is adding extra air from the air box you can gain some increase in air box pressure when at speed.
Keep in mind also that with the clean air system in place, any air/fuel sensors or dataloggers on the bike will show a leaner running engine causing you to tune your bike and adust the fuel system too rich. This can only be prevented by eliminating the clean air system and all associated hoses.