make sure that the wire that got pinched was actually a ground. If it is a b+ coming from the pcm and it gets grounded, the pcm with short and fry something internally. This all leading to tons of problems that are unexplainable...I know this from personal expeirence lol.

 

Check and make sure you don't have any power sources shoting out. My buddy had the same issue with his camaro and it was the wires to the starter shorting out.