Update:
I saw in a wiring diagram someone had posted up here, that those wires appear to be for a security/alarm system. I didn't cut them out though; I just wrapped the connector in plastic, taped it all up, and tucked it in the battery compartment.
My PDI is completed and I've only tested the bike around the block. I'm anxiously awaiting the paperwork so I can register it and get out on the road.