A lot of what you asked is for opinion, and I will give ya mine.
One of the best things about these Jeeps is their ability to mix and match.
Look for a V-8. Most have a 360 in them, mine had a 304. Not sure if the 304 ever actually came in them from the factory.IF you look at the earlier J trucks, you can fine some with a Buick 350 and a Turbo 400. In my opinion the best set up as far as the auto's go. But for reliability sake, I would look for one with a T-18 trans in it. It has the low first gear. I am thinking in the 6.32 range as far as 1st gear ration. It will have a Dana 20 T case behind it. The tranny should give you really good service. The Dana 20 is also a great t case. Biggest draw back is the gear in less than 2.0, and the shifter is kinda crappy, but, you can get an after market twin stick shifter that will make all the difference in the world.
As far as I know all the J-10 trucks came with a Dana 44 front and rear. I do know some waggys had an AMC 20 in the rear. Good axle in the waggy form, weak link being the axles tubes. AN easy upgrade to Chevy One tons if you want to make it pretty bomb proof.
Thinks known and common to go wrong with them, and things to look at.
Floor boards are almost always rusted out. The door seals leak and they hold water till they rust through.
Rust behind front bumper
Window fuzzys gone or worn out
windows won't roll up or down
rust in the bed about anywhere inside or out.
Chopped up wiring harness
Dashes crack and bow up in most
Heater controls broken
Seats worn out and seat belt don't work right.
Full size Cherokee doors, seats will work in these
Arm rests missing or broken
Later models come with a Delco Alternator, earlier years had the Motorola's which only came in a 40 amp version
Radiator straps tend to come un brazed, easy fix though.
Very easy to put OBA with donor brackets and Compressor from a Wagoneer.
Wiper switches tend to go bad as do the headlight switch
Instrument panel plastic covers tend to come off and slide down
Tail gate latches are also know to break.
All I can think of for now. But for the record.
I have always liked the J truck styling.