Long story short, I have two 98 mustangs that are about ready to be scrapped. I am really hoping to get one of them up and running but am getting frustrated with all the issues I have had between the two cars. Currently, the one I would like to fix, has a fried PCM and I thought I could just swap them out, but the other car (the parts car) had transmission issues and I can't get that code to clear off the PCM, which is causing the car I want to fix to stay in limp mode. I know there was nothing wrong with the transmission on this car and for sure the code is from the other car. I called dealership to see how much it would cost to flash it, but was informed the numbers on the two computers need to match exactly and they would need to whole car down there. I paid 900 for this car and don't want to spend twice that in repairs. I can't drive it in its current state and would have to tow it, which I don't want to do if it is going to be for nothing.

So my questions to you fine folks are as follows:
Does anybody have experience swapping PCM's? If my numbers don't match would I be taking too big a risk purchasing one off the internet? And what about that bothersome PATS? Neither of my cars came to me with the chip keys, both cars have been rewired by previous owners, so would a new PCM cause starting issues because I don't have a chip key?