1996 Chevy Lumina Lumina: Check Engine Trans code.

Transmission problem
1996 Chevy Lumina Automatic 136, 00 miles

We have a 1996 Chevy Lumina. About 136,000 miles. Two weeks ago I got the transmission fluid exchanged. About a week ago I was driving home, about 2 miles total distance, and I glanced down to notice the temperature gauge was just under the red. I parked at home and looked at the radiator overflow tank, it was completely empty. I filled it, let the car sit for five hours, and checked again. Empty, with no puddle. Car sat again, checked, and empty again. I took the car in and they replaced the radiator bypass hose, as well as the serpentine belt. After they replaced the hose they went to rerun pressure checks and couldn't get the two radiator fans to turn on. After a day and a half it was determined that our computer was shot, due to a faulty wire-which cause all the other problems as well. They put in a used computer and reran tests. Instead of looking for the faulty wire, they explained they could run the fans off the battery. We got the car back and it didn't overheat. However, our first time on the interstate, over 50 mph, the check engine light came on. We took it in and it was a transmission code. Mechanic said he thinks the transmission wasn't getting cooled properly because our fans weren't working the way they should have when the wire was bad. I checked the fluid, it was still clean and full. It also doesn't smell burnt. My question, does this mean we need to replace the transmission? Or can a repair be done to the transmission cooling line? Could we just change the filter and fluid again? Could this have happened because the mechanic bypassed the wiring? What should be our next course of action?