I always check the frame horns for rust or patching. The body can always be changed but frame problems , can stop a project in their tracks. IMO, go with the 4.0. the power and torque Is good for tires up to 31" with factory gearing.
Both soft and hard top. Soft tops get destroyed in the winter. I've got one as a dd with 33s with stock gearing and a 4.0. It's a little sluggish accelerating so 31s would be good with stock gears. If you don't mind the rough ride of a yj then use it as a dd. I grew up with a cj so I'm used to it lol