I recenntly updated my 98 PCM to the newer style 01 PCM. I also added the 01 85mm MAF and am in process of cleaning up for new tune. Anyone intersted in this project effort results I would be happy to help you out. Not that hard, but scary and I got the engine started and recalibrated fairly straight forward. Bottom line it can be done and is a worthy project.

What else needs to be done besides re-wiring the harness? DO any of the sensors need to be swapped to the newer versions? Did you lose and functioning systems, I've heard that the EVAP is a problem when going from 98 -> 01.

Yes the EVAP sensor can be wired up but is not comnpatible, also the 98 harness has no wiring for a Fuel Tank pressure sensor. That code is also being thrown. The 98 has not such sensor so I didn;t even have a wire to use. Options are add the sensor and the wire for what I don't know or use LS1 Edit to skip these codes from reporting.
All other sensors seem to be fine. Had to relearn the BCM and recal the cam. Damn car runs great. Need to retune but has run fine for three weeks. Gas Gage issue reoccured but it could be winter gas, I tried some additives no luck yet.
I also added the 85mm MAF but had to use my old 98 bridge and adapter cable to use 98 IAT. I have the Temp sensor in the MAF so I ordered a diff cable to use it in the 98 harness, then I can go to a 01 Air Bridge for better MAF fitment. MAllet has the 01 Air Bridges brand new takeoffs at about 1/2 factory cost.