I ran the wires to the flap motor tonight. I put a two position molex connector on the wires so that the motor can be easily disconnected if it needs to come out. There will also be a second connector here for the three pins from the flap position sensor.
I cut away a chunk of the forward end of the aft tunnel cover (basically the part that will be inside the flap motor housing.
This lets the wire that runs down the flap tunnel pass through the rear spar before coming up behind the flap weldment. All of this will be secured by some wire tie mounts to keep it from coming in contact with the weldment.