Ok I have an 1995 Saturn sl2 stick shift and I had an auto matic PCM/ecu from same year same model car dohc jus like mine but for an auto and I put it on and it makes my car run much better smoother but it has the check engine light on because of no transmission input of course and the shift up light but my question is why does it run better with the auto PCM/ecu ???

 

Most probably the reason you changed it because there was something wrong with the origninal that affected how the engine ran.
or
you got lucky
or
magic?

 

prob because the pcm, deprived of auto tranny input, is in some closed loop limp mode that happens to be better than he closed loop control you were getting with the proper PCM in the car