2005, Chevy Malibu, how do I check that the right computer was reinstalled

Try a local shop for the flash. It'll cost about $100 but your vehicle won't run without it! A dealer may not want to go near a junkyard PCM! If it were me, I'd buy a rebuilt PCM from your local auto parts store, have it flashed at a local shop, and turn in the junkyard PCM for the core charge. Yes, it will cost more, but you'll have the correct part with the correct programming. Consider it a lesson learned! Hope that helps! Jim