Ok so some progress… Flash it to pin 42. Now I have on and off at least. I do not however have variable voltage. It turns on at 51% – 100% it is off at 0% – 50%. Always sitting at approximately 4.5v it does not go above that voltage.
I completed all the steps I outlined. The laser burns but it seems to be stuck at max power I guess if 42 is 4.5 volts. Is the mega board toast? Surprisingly enough after hitting it with the 12v polarity reversed the driver still seems to function normally.