reprogramming computer

just got my car out of the shop and the mechanic says he thinks that i need to have the computer reprogammed(flashed?) sometimes it runs ok other times it barely moves(usually when cold) i bought this car with a dead engine and swapped a running 97 CV motor and transmission,never ran right since.their is a sticker on the radiator support saying it was reprogrammed by ford when it was one year old.could this be the problem?
local dealership wants 70 dollars to flash the puter.if i can find a puter art the local U-pull it ...it would only cost 30 dollars.would the puter just swap over with no problems?