that's a great idea...a CJ3A would be a great weekend toy for around town....a CJ2A would be my pick though (just prefer the less high hood and closer MB resemblance).
i am starting a CJ5 build myself working with a frame and tub only and building from there. i am planning the same drivetrain combo. i had a blazer with the 4.3L and loved that engine. when i got the CJ5, i immediately knew that was the engine i wanted to run in it. i was originally planning to restore it to stock-like specs because it was about 99% complete and stock when i got it. however, i realized that while i have always wanted to restore an old jeep, the CJ5 was never that jeep. so i will be building it for wheeling instead.
as far as a project from scratch goes, while i have not actually completed one yet, a Jeep seems like it would be about the easiest to do (or perhaps a VW Bug).
you can make something like this as cheap (within reason) or expensive as you want. certain things will play as factors in overall cost...new vs. old/original. sometimes with these old jeeps, it's easist to start with brand new reproduction than trying to repair something old and original. on the other hand, just as easily, you may be able to find an original tub in good enough condition to repair. replacement body panels are made for most body parts of these older jeeps. it seems there are certain areas that are prone to rust and rot, so there is an aftermarket for these areas.
i'm kind of in the same boat as far as skills with these things go. i can't weld and i don't have the tools to fab my own metal stuff so a lot of things will need to be 'hired out' or i will need to find a local jeeper willing to lend a hand. when it comes to things like that, the cost of a build goes up. so in the case of say, repairing an original body, for the less skilled or tooled of us, a new tub may be worth an added expense. yada yada...you get the point.
for a build like you're talking, i would expect to spend no less than $10k. you may be able to cut some corners here and there, but it could easily go way over that without the flinch of an eye.
for the build that i have planned, using mostly non-stock parts (only the frame and tub will be original), i am looking at about $15k for the build. that is a reasonable estimate i think, but i know it could easily go higher depending on how much i end up having to 'hire out' vs getting friends to help with.