Power commander problems

Check the little vac. line off the rear of the airbox, change the plugs. I ran mine w/o the line on it for no more than 5 mins, it fouled 2 plugs so bad it was only running on the other 2 cyls. Triple check all vac lines off the airbox when reinstalling.
 
(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?
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I would not use the exhaust tip method. It will just give you a false reading
 
I have the same problem with my 2000 model. Just bought it last week. Stumbles at low rpms and clears up around 6k. Ran with pc usb and without changed plugs, fuel lines, check all vacuum hoses still nothing. I am no idiot but this thing is kicking my a%#. The only thing I can tell you is the 99 and 2000 models are notorius for clogging the fuel screens. There is one at the fuel pump one where fuel pressure regulator meets fuel pump and one on each fuel injector. This is my last resort but it is hard to do with a 10 day old baby in the house now. Try to clean these screens and change fuel filter. Good Luck
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Mr Brown wins!

It was the small vac pipe to the airbox that was dislodged. It had come to rest between the injector bodies, and i had missed it.
Thanks for all your replies guys, i appreciate your help.

Got a custom map installed now, and will block the pair valve.
It now FLIES!!
hOORAY for Akrapovic!
 
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