I know I'm a little late to the party, but on the T-Case info, I've got a bit of experience.
You 'SHOULD' be fine running a D20 with your stock offset axle if you decide to go that route.I would not go with a D18. Too noisy, and they have weak links, especially on a big heavy truck like this.
So, as mentioned if you are rebuilding your TH400, you'll need a D20 output shaft, and the spacer that goes between the transmission and the t-case. Likely would be your best bed to get a whole transmission from a D20 rig, and rebuild that.
As far as the offset axle is concerned, heres what I can tell you. There are a few different options out there for passenger side drop. You Narrow track q-trac axles, narrow track D20 axles, and "all" wide track axles.
If you had a NT rig, wagoneer or cherokee, your rear axle was determined by the t-case you had. Q-track = offset, D20 = centered (or mostly centered, my 73 axle wasnt fully centered because of the gas tank). If you had a WT rig, it came with the same axle, regardless of D20 or Q-Trac. There is a reason for this.
On an NT q-trac axle, the driver side tube on the axle is the same as on a WT axle. The difference is on a WT axle, the passenger side is 2" longer. they didnt add 1" to each side, they added 2" to the right side. What this means, is in order to center the wheel mounting sufaces, they shifted the axle 1" to the driver side. So, if the driver side tube is the same length, and they shifter the whole thing 1" to the left, that means your Diff comes 1" closer to the center.
This, the WT axles are only offset by about 4.5" If memory serves. This is only about 1.5" more than a stock D20 rear axle (at least in the case of my 73, I'm not positive if the 74+ rear D44's for D20's were still offset, but i think so). They came from the factory with the same 4.5" offset for any WT FSJ, regardless of transfer case. The NT Q-trac axles have the most offset. This is because the passenger side tube is 2" shorter than the WT axles and the other side is the same, so it's got an extra inch of offset when centered under the truck, about 5.5" from center, IIRC.
So, have no fear about running a D20 with a WT offset axle, its not offset as far as you think, and thats the way it would have come from the factory.
Just so you know, I'm running (due to stupidity) a NT Q-Trac axle under my rig, with a D20. Its got something stupid like 5.5" of offset, my driveline angle is awful. However, several folks on IFSJA have done this swap, and everything is fine. I was initially worried because not only is it offset so far, but I'm lifted 4" which adds to the issue. I can cruise at 75mph on the highway with no vibes. The ONLY time I get vibes because of the stupid compound angle is when I'm doing 70ish and put the pedal to the floor. I'm assuming its because the engine shifts under heavy load and exacerbates the angle. Even then, the vibes are not bad at all.
I'll simply carry spare u joints, and inspect my u joints once a year, rather than never.
Hope that helps. Basically I'm saying I'm running more offset, with the same lift you are hoping to have, and it's fine. There are other folks on IFSJA that have swapped D20's under their QT Cherokees and whatnot, and they are fine as well.
