The Power Commander III, aka...commander crap, is usually hanging down by the tool kit under the left side cover, and plugs in under the seat on top of the battery cover. Big white plug about 4 inches wide, just unplug it and find the original one right there next to it, plug it in. That bypasses it. If that fixes your problem you've found the the culprit.
2003 VTX 1800R