you have to have some backpressure when the exhaust is coming out of the muffler. with stock, you have too much backpressure. when you go with an aftermarket exhaust, you relieve some of that backpressure but no all of it. with a dual exhaust, you lose pretty much all of it, and then you will start to lose power.
im sure johnnyb can help you out on this one. hes pretty good about this stuff.