I wanted to give an update. I am still having the issue.
If i use the key to start the truck it works flawless without any issues or codes. If i use the remote key fob, it sets the same transmission codes. I even tried using the remote start, then pushing the brake shutting the truck off, then inserting the key and starting up. It still sets the codes. I went by Best buy that had installed it 2 years ago to ask some questions. There is a sign by the install door stating hours TBD once an installer is hired. I have the proper voltage from the ignition switch to the harness at the pan. Proper voltage across the Ign 0 fuse.
I am going to try it with the key in the ignition and in the on position and use the remote. If it does not set the codes I am going to assume the remote bypass has failed or the ignition switch is bad.