Well, 8 hours later and I have it running. 

Get this, it burned the wires all the way back to the fuel pump.  It started to melt the plug going into the fuel pump, a few seconds more and I would have been dead.

I had to make an entirely new harness for the charging system, every ground was burned, everywhere.  Switches and relays are blown everywhere.  I can't get any of my lights to stay on, they flicker on and off.  I had to totally reconfigure almost everything.  There are so many jumpers in my fuse/relay panel that it's not even funny. 

I now have a switch to turn my fuel pump and ECU on.  I guess it's kind of cool, I could leave my keys in the truck, but no one would ever figure out how to start it.