nyblack89stang

hello i have an 89 mustang gt 5spd with the a9l computer my problem is every time i restart the car it runs ruff and almost dies under load and pops and kicks seem to be for the first couple of mins hot or cold. my check engine light is on but when i try to do a self test it doesn't give me any codes could the memory in the computer be shot to me it seems like it is reprogramming every time it restarts. i also have msd 6gal ignition could that be the problem? any input would be great because im out of ideas thanks.