I installed a Chev. 350 in my '89 MJ. It's great! It was easy, is reliable, has tons of power, and gets better mileage than my 4.0. I used Novak's bolt-in aluminum radiator with two 4.0 electric fans. Running 35" tires, it has never gone above 210 degrees.
The items to do the swap financially made more sense to me versus a stroker kit, etc.
Radiator - $560
Bolt-in motor mounts (Novak) - $200
Coated headers - $385
Adapter from 700R4 to t-case - $500
Engine - $250
Rebuilt 700R4 - $1000
Fans - $20
Tach converter (Dakota Digital) - $80
Lokar shifter in factory MJ console - $300
Total = $3300 (and this wasn't really cutting any corners)
There were no mods needed to the firewall, grill, hood, and I used all the factory gauges. It came together really nice and is now far more reliable than it was before.
My understanding is you can use the AW4. To control it, you simply need to retain the TCU under the dash.