I had the same questions with respect to exhaust, flow, and FE.
The best rule of thumb to use: "Stock is Best". It was finely tuned by experts -- any change in that system will effect the bottom line. Quiet is good.
Here are some great links on the Science and myths of Exhaust, by Team-Integra.net:
Exhaust Basics
Advanced Exhaust Tech I
Advanced Exhaust Tech II
RH77