All Aw4s have some computer help. I know that there is a difference between the 1994 XJ computer that I lifted and the 1999 tranny that I have. Nothing major. Some time around when they integrated the TCU with ODBII they added an input speed sensor in the front of the tranny. That's the only extra thing I found.
So far it looks like the older computer will controll the newer tranny without any issues. (I'll know in a week when I install it). The newer computer will run without the ODBII (well, ccd bus) hooked up. Looks like its just used for error reporting to scan tools. So you should be able to splice the newer odbII style controller with provisions for the input speed sensor into an older XJ, but there doesn't appear to be much need.
I don't think the newer computer will be very happy with an older tranny due to the lack of that sensor, but that's not a problem you have.
To mate the 1991 tranny computer to a newer tranny you will need to do some wiring harness work as the connectors changed, but its not very complicated. If you still have the old 1991 tranny you should be able to swap in its harness to the newer tranny and call it good.
Jason