Transmission clunks/stuck in third

I have a 94 SL2 and it has become stuck in third gear. I've replaced the transmission, but the problem still remains. Every time that I switch it into reverse or from reverse into drive, it has a telltale clunk and shakes a bit. I know that it's stuck in "limp in" mode and have tried getting the code from the computer, but it isn't telling me anything that seems to work. If the actual transmission itself isn't bad, what else could be the problem?