Engine Replaced, Now wont shift? Help
 

Ok, so my uncle bought a 2012 mazda 3, with a 2.5l engine with automatic transmission from an auto auction with the intent to fix the car up. The car had some heating issues and on the return trip home, the car got so hot the engine finally stopped and never restarted. so the engine was replaced with a used engine from another 2.5l engine that was suppose to be a "exact replacement". Now that the engine is replaced and instated by a mechanic, now the transmission wont shift into any gears except reverse and 1st. is it possible that the computer for the engine also controls the transmission as well? has anyone had these kind of issues? The transmission worked fine before the engine was replaced.