Electronics are getting easier by the day on the new hemi's if you have an ECU and a wiring harness for the new hemi you can get it flashed and run a drive by wire and its not that tough. The 5.7's are still a little more expensive than the 5.2/5.9 but they are getting closer and closer by the day.

If I am buying it Dave, I would go with the Fatman frontend if I am fabbing it up (like I got with my 39 Plymouth and with what I am looking at for my 48 Panel) I am going Dakota.
If you change to the dakota and the 5.2/5.9 the motor mounts/geometry are already there you just need to see if you can get the engine placement to work with your firewall. I am using a 5.7L that I just picked up a couple weeks back but I haven't decided what to do about the electronics because I am leaning towards a 392 stroker kit, with 6.1 heads and would like to put a traditional looking intake and throttle body (XV has a nice one) on the car. The Tranny I have now is a 518 OD four speed but I am see if I can find a 5spd od auto for it. Electronics wise, I visited Speed and Performance in Mena, AR a month or so ago when I was down there for work and they know their stuff and have been some of the first to do these transplants. But at the same time, XV seems to be doing more with modified motors, while I have also seen a transplant of a 5.7 in a dakota where the guy did all the wiring himself combining harnesses from both the dakota and the 5.7 donor truck. I am not a wiring guru so this seemed daunting to me, so I will be buying a kit and I heard that there are a couple of guys that do most of these kits that the retailers are selling and you can buy straight from them.

Rear end wise I am either using a dakota 8 1/4 (which I will need to convert for the current six lug back to the five lug with axles etc) or I am thinking about a FORD 8.8 out of a Explorer or Mustang to get the 3.73 gears and rear disk brakes but I am also thinking an early 90's Grand Cherokee would have the same gears and disk brakes (may depend on what the yards have when I go look), either can be provisioned to give you an e-brake pretty easily. But I also need to figure out what width rear I want to end up running because there is a ton of room in those fenders so it may be possible to run 10" or 12" wides if I can find the right offset without narrowing the rear-end.

I am right behind/ahead of you with this same build Dave, I am dealing with a 39 Plymouth 4 dr but I want it to be a comfortable cruizer that I can take across country if the urge hits. I am lucky enough to already have the front clip done for me so that choice has been made but I am still working out the rest. I just want to be sure if necessary I can pull into just about any town and get the parts for the drive train if it brakes down.