Having the ECM flashed

What is your question?

I put a new motor in my car but took the whole top of the motor and put it on the one I put in. All the electronics that was on my old engine was switched to the one in it now. The car will start but idles up and down, give it fuel and it sounds like it wants to quit. I was told I need to flash the ECM. If the electrical is all the original hooking up this new motor, why do I need to have it flashed?