Hey Kevin, gonna try to answer as much as possible here. I never did a write-up on it. I just simply ran out of time and motivation. This is why I started this thread -- it will be as close to a writeup as I will prob do.
The following answers reflect my experience only and are not necessarily a bible to follow. You should do lots of research and make sure you truly want to commit the time and money before starting. While its a straightforward swap and not terribly hard, prepare to be somewhat nickel and dimes to death along the way.
12V or 24V?
In my opinion, a 12V is the best way to go for simplicity. They are easy to work on, lots of parts laying around for them, lots of easy mods, very proven, no need to worry about the "53" block, and so on. It was the best option for me at the time. It is not necessarily going to be easier for electrical reason since you will still need to swap wiring harnesses (which was a huge PITA for me) -- again, it was just the simplicity of the 12V I was after.
Do you know if the 2500 transmission will mount the same as the old 1500 transmission? Do you think current linkage would also work?
Tranny mount is the same as well as the crossmember. I am not sure on the linkages, although I am sure they will prob work or need some light minor modification.
From reading the post, I will also plan on swapping out the front axle but will the current rear axle work?
Current rear axle will work, but may not work for long. I ram around on the 1/2 ton stuff for a few months until the front coils finally gave way. I would seriously suggest getting one ton axles, esp for the front. A rear Dana 60, 70, or 80 is cheap and an easy install.
Will the transfer case need to be swapped?
Yep -- you will need to find a 23 spline tcase to fit an auto trans. The poor 231 tcase out the gasser would not like the diesel power anyway.
Will the current drive shafts need to be replaced?
This will depend -- they don't need replaced, but you may need them lengthened or shortened depending on current lift and other mods. I used the rear 1/2 ton driveshaft and ujoints the whole time I ran one ton axles. I pulled the yoke off the 9.25 axle and installed it on the Dana 70 from the one ton. Splines on the yoke were the same. I would recommend a driveshaft out of a diesel since the ujoints are beefier, but I made do with what I had. I was budgeting somewhat when I did mine and did not want to have to get a new driveshaft made.
Front driveshaft should be fine tho -- look in a junkyard if yours doesnt work for one out of a diesel with your same cab/bed configuration.
Will the radiator need to be swapped? I'm a little confused on intercooler, do all CTD have an intercooler or were they added sometime later?
Yes - here is where having a complete donor truck was nice. While the radiator may work, I would want all the cooling power I could get to keep my investment running cool.
I would strongly recommend finding a cummins with an intercooler. I can't remember what year of first gens they were added in (maybe 89 or 91). Someone else can chime in.
Will the CTD and transmission from a generation 1 dodge fit correctly in a 1998 or should I only look at gen 2 donors?
I would find a second gen motor since more of the electrical is the same, esp behind the dash. The first gen motor will fit in just fine tho. I am unsure if the earily first gen trannies will bolt up to the 2nd gen crossmember tho. That would be an easy fix with minor modification if it didnt.
Finding a complete donor truck is the way to go, but I know its damn near impossible. I got lucky with mine -- but I also looked for a year and constantly made calls. The complete truck just saves you all kinds of time and money on parts, while giving you a chance to sell off the rest and recoup some money. It can be easily done without a donor truck handy, but this is where you research first and getting the needed parts before starting will come into play. Some of the longest delays came from waiting for the dealer to get my parts in -- and the constant run to parts stores got old REAL FAST.
GOOD LUCK.