As far as the 99 PCM controlling the 65E, I'm not sure. But, I don't see why not due to them being in the same year range.
I believe you would have problems with the 97 PCM in a 99 body. Things like your instrument cluster could be different, your fuel sending unit, HVAC, etc.
When your vehicle is inspected every year, do they hook it up to a computer to check emissions? Not the exhaust, but the computer? If it sees a different year/VIN, it could fail.