Reprograming VIN into PCM????

I recently had a new PCM installed on my 96 Eclipse GS. OR acturally a salvaged one. My car wasnt firing in 1st and 4th cylinder, took it to a shop and they replaced the PCM and it started firing in all cylinders. But now it runs rough. in studders in idel every once in a while and when accelerating in drops pick up at 5000rpms and it suppose to red line at 6500rpm with no drop. I was told I needed to get my specific VIN programmed into the new PCM. Has anybody ever heard of having these reprogrammed with the VIN, if not any idea of what it might be. I have had the plugs and wires and coil replaced. next trouble shot would be the PCM.

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Vehicle Identification Number being programmed into the ecu would have nothing to do with how it runs. And as far as I know, they still are not doing this, at least with the turbo cars. I am hearing about it happening on the EVO9s, but they've been saying this for 10 years for whatever generation is out next. At any rate, I can't see how it would be related to how the motor runs, unless the factory specifically wanted the VIN set in the ecu and this is the only way they could make poeple do it. Highly unlikely though.