Backfiring is the sound of fuel being burned in the muffler. To happen, you need unburned fuel, an ignition source (hot metal, exhaust gases) and air. When you quickly chop the throttle and decellerate you send the greatest amount of unburned fuel to the exhaust and this is when the condition is the worst.
An unburned fuel condition is usually caused by a LEAN condition. What happens is that a lean mixture will fail to ignite consistently. This, in turn allows some un-burnt fuel to get into the exhaust pipes. Then when the engine does fire, these un-burnt gasses are ignited in the exhaust pipe, causing the backfire.
Any EPROM chip or Power Commander fuel map that is not well-matched to the exhaust system can produce an air/fuel mixture that results in more unburned fuel being sent through the exhaust pipe and muffler. So a chip change alone can cause backfiring, especially during closed-throttle deceleration.
The best approach is to put the exhaust cans on and have your dealer re-adjust the CO level to compensate for any increased airflow. There's a CO trimmer screw adjustment on some earlier bike's ECUs that provides for limited changes in fuel mixture at idle (with lesser effects across the RPM range). Go easy, a half-turn on the screw is usually all that’s needed. Any more may decrease drivability. A Mathesis is needed to set up a 749 CO.
Always a good measure of fuel mixture is to check the color of the inside of the tailpipe. After a few hundred miles it should be medium-to-dark gray, not black or sooty.
Slip-ons as a rule won’t change air flow very much. The most common situation is that a newly-installed exhaust pipe or slip-on is not fitting properly. Aftermarket pipes are not a precision fit and often they let in combustion air that, when mixed with unburned fuel, results in the fuel being burned in the muffler. If this is the case, use a high temperature silicon sealant at the joint to the slip-on to keep the air out.
I recommend Permatex Ultra-Copper high temp RTV silicone gasket maker #101BR for the aftermarket slip-on system joints. Good to 700?F intermittent. Available in auto parts stores.
http://www.permatex.com/products/pro...tem_no =81878 Full length, larger diameter exhaust systems are designed to flow better so more air through the valves without added fuel will usually give you a lean condition. You need to check the air/fuel ratio on a dyno to be sure.