2001 Saturn SC1 Transmission Problems

I own a 2001 Automatic Saturn SC1 and I have been having major issues with the transmission. I have had my transmission replaced before and then about eight months ago my transmission broke again. I brought it to a mechanic and after 2 weeks he also said that my engine was bad. He replaced my engine with the SL2 Engine which is a twin cam engine. My car is standardly equipped with a single cam engine. He put in a new transmission and the vehicle is having issues. sometimes the car shifts fine and other times it wont shift out of first gear. the mechanic said he tried 4 transmission and none of them worked. He is now returning to me my vehicle afer 8 months and the car still doesnt shift properly. Does anyone have any Ideas of what it might be?? The mechanic said it might be a wiring issue but he is moving out of the state and refuses to work on the car any longer.