Bumping it up.
So today I installed a new box- and the problem doesn't seem to be the box- because I still don't have spark.
So we ran voltage tests on everything- pushing the bike around while my buddy Matt held his tester. The results- The Green wire into the box provides constant voltage as does the yellow lighting wire. They provided no voltage at all- no pulses, nothing.
I also pulled the stator and the coils and reinstalled them, and we checked the continuity on the coils and they are intact.
Oh and I put in another redundant ground.
What do you think? Bad pickups? I honestly have no idea. I think I got a bad unit- 2 bones down the drain?