The Mallory tech that worked on my box called me again today, since I had left my number to the secretary or whoever it was I talked to. She was friendly which I suppose is refreshing at this point.
She tells me that they found nothing wrong with my box.
They did fix the whole harness polarity issue though.
I'm not sure what going on here. I can plug an HEI module into the exact same wires the box uses and the truck will fire on the first turn of the starter. I suppose we'll see what happens when I get the box back.