fixen

I have a 1994 Chevy Silverado 6.5 Turbo Diesel. I took it to GM because I had a new engine put in it about a year ago and it was blowing black smoke. I also had the transmission rebuilt at Amco. GM put it on an ODB2 code reader and it showed 3 codes. 68, which means transmission component slipping, 39, which is TCC stuck off, and 83, which is TCC TWC cylanoid circuit. How hard are these things to change? I am going to take it to Amco because the transmission is still under warranty. What questions should I ask them? Will this transmission need to be removed and rebuilt again? Any help on any of these matters would be greatly appreciated. Thanks.