what you would need to do is get the obd2 computer tuned to the SHO motor. What would be involved is getting all the tables (spark timing, injector timing, etc. etc.) for the SHO pcm and making sure you could make all the needed changes to the obd2 pcm. That would be the only way to have a obd2 pcm control the car, since the SHO was never offered with obd2 from the factory.
the emission requirements for 2000 were more strict than the 89-95 ones, but the SHO motor was pretty clean so I think a decent running SHO motor would pass 2000 emissions requirements. You should be able to find out what the various requirements are for the years 1995 and 2000, and see how different they were. I do recall that a decent running SHO would put out 10%-25% of the limits for 94.
I dug through my records, and found a report on my red 94 SHO from 06:
HC limit 2.0, actual 0.31
CO limit 20.0, actual 4.84
NOx limit 6.0, actual 1.49
I found a report from my 97 TBird,
HC limit 1.20
CO limit 15.0
NOx limit 2.0
So, the 94 would pass 97 requirements, but I don't know how much tighter the requirements got by 2000.