They have an article on an AOD - T5 swap. The last step they show is swapping the computers out. From what I have always been told you don't have to swap them do you?
James, from what I have read, I agree with the others here. FWIW, the car owner in that article is a member here - we could ask him why the puters were swapped.
I think it was because a shop did it, and it was for an article, so they chose to 'properly' swap all 5 speed related components.
I personally have run both the Auto (A9P) & the 5 speed (A9L) in my Mustang with a Tremec 3550 5 speed. I didn't notice any real difference on the street, and never went to the strip.