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When it comes to isolating a rotation, noise or any other mechanical issue (not spark or fuel related) on a DOO simply remove the pump. "Break the system in half" and save a lot of guess work. If the rotational issue is still in the motor, well, I'm sorry since that never ends well and involves taking the motor apart. If it is in the pump, you still have to take the pump apart, but that is simple and cheap (when compared to the motor).
Keep us up to date on what you find. I hope it's something simple.