How do I troubleshoot a transmission problem if I get no codes?

I had a poor mechanic shop work an overheat problem, they replaced my cooling fan motor ( supposedly with a new one) and then told me it was the Powertrain Control Module which controlks it that was bad. So they hotwired it to run anytime the engine was running, assuring me that they had done this many times and it worked perfectly. On the road my car just shut down completely, after some investigation, I found that they ran a lead from the EEC relay power to the fan motor wire. The junk fan motor they had put on had burned up, drawn too much power and burned completely through my EEC relay wire shutting everything down. I reconnected the EEC wire but as soon as I reached about 30 MPH and the car went to shift into 3rd it locked up low and the high clutch packs and burned up my high clutch packs. I've rebuilt the transmission and relaced the fan motor, both relays, and checked aqll the fuses ect. but cannot find the problem with shifting. It runs fine in 1st or 2nd I just cannot use drive. I'm getting no codes and everything is running great, even the fan motor.