Does the fuel pump prime when you turn the key on?
If not, that could be a problem also.
Have you jumpered the green service connector and switched the bike on to view the error codes? It may give a clue (or not).
And yes I'd try disconnecting the power commander from the system to test.
Of course it may not run perfect, but it may helpful to know it was or wasn't the problem.
If you have the PCIIIUSB, the you only have to reconnect the gray connectors on the left side of the engine.
If you have a PCIIIr, then you'll also have reconnect the red OEM connectors from the pulse generator coming out of the alternator at the lower front on the engine.
Last edited by SubSailor; 05-16-2010 at 08:16 PM.