Unfortunitly, you are kind of in the mercy of the codes to find problems.
I added a remote starter that initially was confusing the transmission computer so i knew what the issue was. I changed the wire that was tied to the starter crank and it was no longer confusing the tranny ECU.
Do you get a D4 flashing when you start the car? The D4 should light up steady when you just start, not flashing.