Have you tried tried switching the polarity of the pickup wires?

I ran into a similar problem last year. I did all the same checks and rechecks you did, no dice.

Posted the problem here and Bob George said to try that. I didn't really even understand what he was referring to at first but then I went back and re-read it. I went out and tried it and voila! Car started right up.

MSD actually makes a note of it in the instructions.