I'm think my next plan of action is to abandon the stock wire runs from the head unit to the amp that I recycled, and run all new wires

Pull the amp out of the car, take it to your friendly stereo shop (or, connect it to your friend's car) and test the hell out of it; or borrow your friend's amp and test it in your car. If I had to guess, I would say you have an amplifier problem. Don't assume that the amp is working properly.

tanstaafl.
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