A 2000 PCM programmed for the NV-3550 manual transmission will still work fine for the AX-15 manual transmission used in 1999 and older TJs. So your PCMs should work, though make sure the PCM for the 2000 is for the type of ignition it has... with a distributor cap and separate ignition wires, or the newer coil rail ignition system that doesn't use a distributor. 2000 was a transition year for the ignition system so just make sure you have the PCM to for your particular ignition system.
The 231 tcase input shaft made for the 1999 is short since it's made for an AX-15. It's not long enough to seal the output shaft opening for the 32RH. That'll let the 32RH dump lots of ATF out its output shaft opening. No worries though, both Teraflex and Summit Racing have extended output shaft seals for the 32RH that work perfectly to seal it to the 231's short input shaft.
At least you'll have access to both Jeeps and can swap parts between them. I did an AX-15 to 32RH conversion on my '97 TJ and had to figure out what additional parts, mounts, etc. I needed as I went.
Also, the hard coolant lines leaving the 2000 32RH may or may not fit your '99, locations of a few things changed where the hard line routing is concerned. The hard lines that came with my used 32RH couldn't be used on my '97, I had to order a set of new hard coolant lines.