Wowo, I learned somethng newq today. I didnt know the 4th gens had a code for the radio..

Anywayy, as far as the trany, mine does it too, warm or cold. but then I use to do alot of N-D4 drops. and I think I fawked it up some. The rough idle, check your front motor mount. mine did that and the mount was broke. to do that you look at the front of the motor in front on the "headers" there is a mount, it has little round rubber covers on each side, flip one back and shine a light on the mount and see if it is brok you will be able to tell the difference.

Good luck BTW mounts run about $75+ from the dealer not sure about a parts store.