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I've read through this entire thread and hope I didn't miss these questions. With a stock balancer I have seen them move as much as 50 degrees. I would definitely check TDC and the mark on the balancer. You didn't mention the type of dist or ignition system. If you are getting a popping throughout the rpm band it sure sounds like ignition. I have seen spark scatter cause this type of problem. Ford went to the larger cap on the later engines to help eliminate scatter. If you are running a small cap look inside for tracks, cracks, or anything out of the ordinary. This may be really dumb but have you checked the firing order? With 2 wires crossed the motor will actually run pretty good but under load you will get the symptoms you have. I like to take the simple approach.
Don
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