I have a 52 CJ3A I am working on fixing up.  I currently have no engine, transmission or transfer case.  I would like to go diesel, and I would like to do so for the least possible (hoping to get the engine and trans from a pick and pull).  What would be recommended options?  I am hoping to use this jeep mainly as a daily driver around town, and I don't want to do any major changes to the engine compartment so that it will fit.

I think the pick and pull selection at this point in time is going to be slim pickin's for a jeep application.  The Kubota's fit nice but most of those aren't going to be much of an improvement in the drivability department and are not something you will likely find in any yard.  There have been a number of Benz 617 conversions and those would definitely be a BIG improvement.  Those no doubt could be found in yards-probably more so in yards specializing in Mercedes and BMW's.  Anything Benz is not going to be cheap either to acquire or to repair and my experience with Benz 5 cylinder turbo's suggests they are certainly not maintenance free (I've had three of them).

A for the big 3 offerings, all are big and heavy.  IMO, all are way too big and too heavy for any early CJ.  In short, no easy picks for this at the present time but I do see some good prospects coming from the new offerings by Chrysler and Ford.  By the time some of those become common in the salvage yards, I sure someone will have an adapter harness to sort out the electronics.

In the meantime, just put a small block chevy in it like just about everyone else does.  It doesn't get any cheaper than those and they do work.

A landcruiser 3B (4 cyl) diesel would work - have to use all Toyota drivetrain. Ditto for the old Nissan diesels. Isuzu makes a good small diesel.

Check out the CJ2APage under modifications. Daniel Buck has a nice write up on his Kubota transplant. He was able to use the Willy T90 and D18 without alterations.