It should be a plug and play. You can keep the existing Trans computer. It's located under the passenger kick panel, but you don't even need to touch it. You should be able to just unplug the two tranny connectors located on the passenger side of the firewall. One connector is the NSS sensor, the other is the solenoid and speed sensor wiring. Follow the two wiring bundles from the tranny to find them. I'm 90% sure the solenoid/speed-sensor wiring harness connector is identical between the 89 and 93. If it's not, can pull the pan and swap in your existing solenoid wiring harness. The NSS wiring connector should be the same, if not just use your existing one.
Electronically, the only thing that changed on the AW4 was in 1996 when the rear output shaft speed sensor changed type and the internal rotor that triggers it went from 1 pulse/rev to 4 pulses/rev. Even that would not be a big deal as I understand you can open the rear of the tranny and swap the rotors and use the existing speed sensor. The wiring harness connector changed in 96 as well.
Mechanically, at some point 4th gear in the AW4 changed from a 0.79 ratio to a 0.75 ratio. I "think" this was in 1991 when the output shaft spline count changed. The difference in 4th gear ratio won't affect the trans computer, but you might notice the 3-4 downshift happens at a 5% higher rpm.
As a reference point, I have a 1999 AW4 in my 89 Comanche. Aside from dealing with the rear speed sensor issue, it was a straight bolt-in. Since I didn't have an 89 tranny to get the correct rotor, I built an electronic box to convert the rear speed sensor output to what the 89 TCU was expecting. A 1989 NSS bolted right on.
I would recommend changing the front and rear seals on the 89 tranny and doing a fluid change. If you have the pan off, you can flush out the "filter" with some carb cleaner. Calling it a filter is a bit of a misnomer as it's really just a fine screen mesh.