I think that I figured it out. I spoke with the crutchfield tech. today, the one who helped me install the remote start system. Seems that I missed a wire. Before he told me that there was no ignition 2 wire. Today he looked over the diagrams again for my truck and found that there is a ignition 2 wire (white). I asked if not hooked up, would it throw tranny codes and he said it would. So I hooked it up and so far so good.
Before I was either getting tranny codes on the "service engine light" or I was getting pending codes. After making the change I immediately checked for codes. There were none showing and none pending. I'm thinking that that did the trick. I hope at least.