2001 Saturn SL2 Is it PCM or the EGR and TCC?

The OBC could not be read for the State Inspection. Took it to a Saturn dealership, let them know it wouldn't pass the inspection because they couldn't communicate with it and they said they would diagnose the problem. Was told the wires had been cut and they fixed it. 36 miles later (driving car home and then to get the state inspection) the car failed the state inspection because it was getting a P0741 error and a P0404 error. I called dealership and they said to drive it for a week to let computer clear. I put some fuel injector cleaner in drove it about 200 miles and took it back to get rechecked for State Inspection and it failed again. So I took it to a certified Transmission repair shop and they said the transmission is shifting fine, but that the code is not being sent and that the PCM gets extremely hot. I took it back to the Saturn dealership and let them know what the transmission specialist had said. They come back and say they are receiving 5 errors. When I check the codes with my OBCII scanner, it only shows 3 errors. The P0741 and then the P040 is now P1404 shows up twice (one with what looks like a pd after the number and one without anything). How do you know who to trust?