I own a 1989 S5 convertible, just recently swapped a S5 Turbo engine in it.
Long story short. Swap runs fine.
but.
The battery was put in backwards by an overenthusiastic friend.
I've already solved the headlight problems caused by this at the Body CPU
and I know the Body computer doesn't have anything to do with the top operation.
but I'm not getting anything from the top

 

you know you problem, i am pretty sure you know the solution to this, test it per the FSM< or replace it with a know working ecu, back probe power wires for... power.

 

yea, I was wondering if there was a known problem that occurs when the battery is reversed.
I just swapped fuses out of the computer behind the driver's side. the 5amp was blown.

 

Then known problem is that it tends to fry circuit boards and pop fuses. If you're lucky, the damage will be kept to a minimum.