[Dezoris]

Short rams and exausts, will hurt your low end, and can cause a rough idle, the exaust is the biggest culpret, because it reduces backpressure, which can cause rough idle. Try running 93 octane fuel and a bottle of fuel injector cleaner, the slick 50 product or valvoline. The best is to have the dealership hook it up to a machine that does it, this can help.
Also how are your spark plugs and wires? How about your distributor?
Was it changed at 30k miles? Also your throttle body should have been cleaned at that time.