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So, I moved the power lead from the factory HU to the antenna lead on the tuner and when I did that the empeg refused to boot.

I'm guessing you moved the wrong wire, or hooked something up wrong, or crossed a wire somewhere, or something. I'm thinking along the lines of a power or signal feed getting hooked up to a ground, or a power feed hooked up to a signal feed. Something like that.

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Then the EMPEG started working and the antenna amp got power but the system made a loud pop when it shut down.

Continued indications of the error above. Also, potential indications of a blown fuse on the empeg main power lead. Or some sort of negative voltage getting applied to something that expects a positivie voltage or vice-versa.
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Tony Fabris