He's right Chet, I was being a wise ass.
Having an 02 harness and an 04 ecu is nothing special. In fact, there is no difference in an 02 or an 04 ecu as they are the same part number. The harnesses can be different, but the changes really don't matter as far as an engine running is concerned, especially since the ecu is the same part. The main differences are the hand controls, which do not affect the engine running quality.
Spencer99, since your posts are so vague, and you don't seem to want to share any information about your bike, but just think the problem will magically be resolved by chance, I made a wise ass comment. Anyone who types,"has anyone asked me what my set up is no" and is the one who asked for help certainly isn't thinking clearly...if you feel someone should ask you what your setup is, why would you not post that in your original post?
Ok, I'll bite, what is your "setup"?
Maybe it is something totally radical like using a GEN2 ECU on it with ony 4 primary injectors, and controling boosted fueling, shifting, adn antilag all in the GEN2 ecu with a custom wiring harness. If that is the case, there probably isn't anyone that would know how to help you, because things like that are way too advanced for all but the most knowledgable folks.
If you are not willing to ensure that a zero map is loaded into the power commander and try it, I got nothin' for ya.
If you are trying to use a PC3r from an 01 bike and have the ignition hooked up, that won't work either. (I know, you probably aren't doing that either and will get pissed off because I suggested it)
Did you screw around with the injector harness at all for any reason? Like swapping pins on both the injector harness side and the main harness side of the connector, making the same wires mate when plugged together, but not being in the stock location.