No, polarity was never a problem, the cables were too short to hook it up the wrong way. The problem was the amount of corrosion on the cable ring lugs and the fact that I stacked them up in a different order than they came off. The corrosion limited the current flow which dropped the voltage enough that it would not keep the main power relay coil energized.
I just sanded the corrosion off and reconnected the cables and everything worked fine.
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