Re: What would cause the 12gauge wire at the Junction box to ground?
SMOKE!!! Melted insulation!! That's a hard short that shouldn't be hard to see. Unwrap that area of the harness and take a look..
If that reveals nothing,my first guess (I hate guessing) is the voltage regulator contacts are stuck - shorting that red wire to ground.. Disconnect the Voltage regulator and, using a test light connected between a battery cable terminal and battery post, check again for the short..
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