I think it would be fun to build a Flatrod out of a TJ. I have been seeing these Jeep based rat rods and creations and I really enjoy them, but honestly the older rigs just dont grab me like the TJ's do, I dunno... just me I guess.
You're already looking at a lot of fab work for a project like this. Adding a couple of motor and transmission mounts isn't going to add that much to it. I'd pick the engine transmission combo you want and not worry about whether it's a bolt in swap or not.