no, auto tranny doesn't matter. you'll just have some extra wires and plugs that you can snip off or zip tie up. 88 efi should be the identical. everything will swap right over. 85 was the first year that the 22re was out in the trucks, and the heads regardless if they were carbed or not are tapped for it with the extra bolt or stud, i don't remeber which.
the 88 efi is unique, it has a different plug on the injectors so if you use a 88 efi harness you'll have to use 88 injectors also.
not 100% sure on the auto tranny wiring but i'm pretty sure you have to wire in the neutral switch so it will start.
