o.k. Here's what I know for sure. Before the rebuild, the car started fine. After, the problem began. I was receiving transmission codes immediately after the rebuild. I took it up to the local parts store where they were doing a free battery and alternator check. Turns out the alternator was only working at low RPM's. i.e. alternator was going bad. As of right now the car is in the shop till the middle of January. I am having them rebuild the alternator to put out 140amps instead of the stock 90 due to the fact i am putting subs in my car. I talked with my tranny guy and told him about this before I gave him my car again. He said that if there is a problem with power to my car, the computers will say there is a problem and start spitting out codes even though there may not be anything wrong. As soon as I get the car back, I will be able to tell everyone if the problems were fixed, or if I need other things fixed. Looks like I answered my own question.