Electrical issues after auto to manual transmission swap

I have just completed a auto to manual conversion on my '00 ZX2. The donor car was a pre-'99.5 (4-wire MAF) car. When I use my pre-'99.5 MAF the a/c compressor runs full time while the '00 PCM (6 wire MAF) prevents the a/c compressor from running at all. The car has had three CCRMs in for testing with the same results. I was wondering if anyone has seen these problems before and could set the record straight on a possible fix.