(Greg B @ Oct. 20 2006,19:30) If the bike is running lean the exhaust tip will be whitish, if rich it will be dark black and you should smell gas.
You should be able to completely remove the PC and the bike should run fine. It may run a little rich but it should idle and be pretty smooth all the way through the RPM range.
When you hooked up the PC did you have to splice it in or does it have plug ends? I would check all the hoses and wires in close proximity to where the PC plugs in.
Changing the exhaust back to stock shouldn't make any difference. Is the exhaust new? Does it have a rat living in it plugging it up?