I need to look at the schematic in a few minutes and see if it's a valid question, but for now I'll ask, did the red run/stop switch on the handlebars get switched by accident?
Edit:
I looked at the schematic, it ain't the red Run/Stop switch.
There is a difference between the Gen II ignition switch recall problems and a Gen I switch. The Gen II ignition switch melted the plastic contact carrier which let the contacts tip and, well, not contact. The Gen I had issues with dirt in the contacts. Someplace between '03 and '04 the ignition switch had and lost a drain hole in the bottom, if your switch has a drain hole you can use a can of cleaner with a 'straw' to shoot cleaner into the switch. Some electrical cleaners can be bad for plastic & paint so be careful.
The ignition switches are made in two halves, the top half is the tumblers which are sealed off from the bottom half with the electrical contacts. Shooting cleaner in the top of the switch will do nothing for an electrical problem.
If you check for ignition voltages, the wires at the ECU connector are sealed, the next best place to check for voltages is at the two couplers from the ignition switch which is a PITA. You will have to raise the tank, remove the rubber shield and fish up around the steering stem to find the couplers. When you turn on the key you should have +12 at the White/Blue wire and the Blue/Yellow wire in the red connector and in the other connector at the Brown wire.
