No changes to the engine or computer (ECC or ECU or whatever you want to call it) when doing a swap from auto to 5 speed. There are some minor wiring change to the starter circuit, but they do not affect engine performance.
Here's a book that will get you started with how the Ford electronic engine control or "computer" works.
Ford Fuel Injection & Electronic Engine Control 1988-1993 by Charles Probst :ISBN 0-8376-0301-3.
It's about $20 from Borders.com see http://www.amazon.com/ . Select boo...very good, and I found it to be very helpful.
Mustang RAK, I just replied to another one of your threads. I think we have a communication issue going on here. Can you please be more specific? Your computer (likely an A9P) is a very good computer. I would be looking elsewhere for the source of your perceived poor performance.
I understand (I had a feeling English was not your first language, and you are still doing better than many of the regulars on here who speak English as their first language).
So you simply don't have the amount of power and torque that you feel you should. You have ok power in 1st gear, but in 2nd gear, you cannot do donuts. Were you ever able to do donuts in second gear?
Do you know how to retrieve the 'trouble codes' from the computer? That is a very good place to begin, if it is something you think you can do with relative ease.