All engines are engineered to run with the system that comes on the bike. Once you change it, the power curve on a dynomometer will show it has changed. While you may not notice any big difference in how you ride your bike, I guarantee you have lost torque and horsepower with any aftermarket system. The only way to fix it is to take the bike to a shop with a dynomometer and have them see where you have drops in the curve and then try to tune it out by programming the ECU (whether it is the stock or an aftermarket ECU). Anyone who thinks they have "more power" with loud pipes is dreaming. This is a case of where perception becomes the person's reality. It sounds loud so they think it has more power. It just isn't the case.
im sure there is a loss of power, but this thing is such a tractor i dont really notice. ive been hit twice this year and will sacrifice a little power to wake up the cagers. i bought the bike used and had a beast of a time pulling the baffles, so im not even sure if i could get the BCT baffles in. they do sound nice though
2007 Vulcan 2000 LT