???
How did it all start? What fuel pump setup did you replace his with? Maybe you got a bad used one?
Have you done a compression check?
Only other thing I can think of is throttle bodies got way out of sync (try swapping with another set) or ECU problem (can try swapping with another ECU from 00 or doing the 01-07 upgrade. If you swap harness, rotor, ECU, throttle bodies, the guy will have a whole new bike and I'd be absolutely lost then too, unless you crack the motor open)