I had to move the motor & trans back on the Dakota frame so the 39 cab & front sheet metal would be in the proper location. I removed a V6 stick and installed a 5.9 gas motor with the electronic controlled auto trans. Just set the mounts to whatever location you need for what ever motor your going to use as you move them rearward. The thing that should be of concern, if you intend on using the 39 truck sheet metal, would be the length of the 5.2 compared to the 3.9 compared to the original flathead 6. The 3.9 will be closer to the same length as the flathead but the 5,2 will be longer. I had to widen the original relief in the firewall to match the V8, and I had to move the radiator forward into the grill housing a couple inches so there was clearance for the V8.
I can't understand for the life of me why all these Mopar people think they need to keep putting carbs on these EFI motors! 89 was the last year of production carbs used by Mopar, and they were crap carbs with a lot of issues. The fuel injection has been in use for many years and most are without problems. If you think you need to put a carb on it, I suppose its your ride.
The trans was pretty simple in 89. I don't believe the computer had any control over it, other then maybe the OD. Most of the electronic stuff on the 89 trans was so the computer knew the vehicle was moving. Gene