Thanks Charles. I have an evo X so the alternator is nowhere near the exhaust. Exhaust is now at the back of the motor.

So one of 3 things I guess.

1. The Alternator is from 2008 and couldn't take the abuse anymore.
2. I plugged my meth kit into the fuse panel into an unused Fuse marked diesel. Possible i could have shorted out the ecu?
3. Somehow the ECU got corrupted while writing to it during tuning.
4. When installing my transmission I had to move my fuse panels out of the way and somehow I shorted a wire

I pulled out the volt meter and checked all the grounds and connections. I dont think its wiring but who knows. New Alternator comes in on Thurs. If that don't work I am staying home