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Continuity or battery voltage at a wire aren't necessarily proof that the wiring is fine. Was it producing charging level voltage at the RR?
You might need to load test the circuits. Get a 12v (at least 15w) lightbulb, unplug the wires, and use them to complete a circuit for the wires (it's easier if you have a powerprobe or something like that). If you find voltage drop, you've found the bad wire. It doesn't take much, unfortunately.
I had a friend who had a bike that was running funny because someone had clamped a tuner onto the wires instead of soldering it in. When they did the clamping, it cut a couple of stands in the wire, just enough that it would get a voltage drop, and throw the sensor reading off. I'd visually inspect all of the wiring, and be absolutely certain all of the connectors are properly connected.
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