I am personally going to be doing a diesel swap in the near future so I thought I'd throw my 2 cents in.
One person in this thread mentioned One little thing that it seems no one else thought to mention, Mercedes.
Mercedes came out with a Wonderful diesel engine called the OM617 in the late 70's and they are known for going well over 500,000 miles (saw a video of a Mercedes with 770,xxx and it still fired up like the day it was new) and supposedly had No major work done, just basic routine maintainence.
I love the Cummins Engines, and I know many have swapped 4bt's and 6bt's into Waggys, cherokees, CJ's, YJ's, etc so don't get me wrong...
But I did a lot of research and put a ton of thought into this before I decided to go with the OM617 Mercedes Turbo Diesel.
3 Liters. 5 Cylinders. No Computers. Around 100hp and around 180ft lbs (the Pump and Boost can be 'turned up' a notch to make over 200ft lbs and Diesels do it at Low Rpm so its perfect for having power on the trail when you need it, IMHO)
For me, a MAJOR deciding factor was that Some of the Mercedes that carry this engine Get over 35mpg and weigh close to 4000 pounds...Our Waggy's are a bit heaver than that, but I still think I can get close to 30mpg when my swap is done.
You can purchase a good running Complete Mercedes 300D (whole car) with everything you'd need for a swap (Transmission, shift linkages/clutch pedal/etc) for less than you can typically purchase a 4bt or 6bt Engine alone.
I am choosing to run a divorced transfercase (NP 205) off of the stock Mercedes Transmission (Preferably a 5 speed in my case, but will work with an OD automatic if thats what comes my way)
Plenty of power, not overweight (compared to the Cummins equipment) and Awesome mileage...plus the possibilities to run it on WVO, Bio, Commercial Diesel, or Even Propane.
Personally, I am not a fan of Ford/Chevy Diesels. I agree with a previous poster that in basically stock trim, they are underpowered and overweight with too many little problems for me to want to mess with. (Fords and Glow Plug problems I have personally experienced in 2 different situations and older chevys wouldn't pull a sick kid off a toilet)
So...if I was in your boat of wanting to do a diesel swap, I would trade the Transmission you have for a divorced transfercase and find a Mercedes 300D to take the powertrain from and slip it in.
I think for me it is going to be a virtually painless engine swap (motor mounts, transmission crossmember, hang a divorced transfercase and have drivelines made). Ive done a few swaps in my life so far and This one should be much easier than the BBC502 in an S-10 I did about 4 years ago.
Just my opinions, when I discoverd the om617 it was literally love at first sight and I'm VERY impressed with their reliability.