starting problems/MANY OTHERS--PLEASE HELP

About 4 months ago, I had a new headunit installed. I hadn't had any problems with it. About 3 weeks ago, I had my transmission rebuilt. Sometimes the car won't start. I bought a battery about 5 months ago so I don't think it could be that. My dad suggested that when the stereo was installed, it screwed up other things. Has anyone else had a problem like this after putting in a new stereo or having their transmission rebuilt? What other problems have people had after getting the car back after having the tranny rebuilt? I have a LOT of problems. You name it, I probably have it. I have all types of codes coming from the car. I'm taking it back to the tranny shop guy to have it looked at again. He thinks it might be a communications problem between the ecu and the tcu. I am so angry. I pay $2200 and it still shifts bad and every other problem imaginable. PLEASE HELP ME.