Seems the connectors inside the plug that goes into the window motor were bent out so it wasn't making a good connection. I couldn't figure out an easy way to bend them back so I just cut the plug off and spliced in the one from the other harness and it works fine so far. I was holding the motor in my hand flipping the window switch and when I tilted the motor it quit. I wiggled the wire and it stopped and started. Compared the two plugs and noticed the difference. Still doesn't explain why I wasn't getting any power at all from the frame harness at different times, perhaps it was tripping the circuit breaker when the connection shorted back and forth.
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