If I was going to build one it depends on what your building it to do? Run stock tires and get ice cream? Or a bit larger tire with mild off road fun? Rock crawling? Mud pit?
If your going to throw bigger rubber and a mild lift on it I wouldn't invest .10 in the rear end that came from factory. Ford explores (not sure if all of them can't remember) came with a ford 8.8 inch 31 spline rearend. If you get one out of a I believe 95 or newer it should have disk brakes on it and they are like 3/4 of an inch narrower if I remember correctly and the spring mounts are like 1/2 inch narrower, its a much stronger axle then the dana 35. Or a great (what I would do upgrade wise) would be a ford 9" tons of aftermarket stuff out there because they've been used it just about every type of racing, plus they are super easy to work on. Gear changes can be done in 40 minutes or less if you have another set up.
Suspension wise it depends upon what you want to do. My personal opinion is not to do the cheap route and put longer shackles on like some guys do, puts a lot of stress on the frame. The YJ that we built in the picture up there had them on it when we got it and we had to unbend the frame where it started to twist.
Engine wise depends upon what you want to do again. I didn't see what year it was to know what 4 banger is in it. Obviously a 4bt would be a sweet set up. But you can also pick up one of the 4.0 inline six's cheap and get fuel injection on top of a nice motor.
Pretty much if you need help or info on them let me know I've been playing with them for over 10 years now and probably will die 10 years younger then I should have from all the rust and mud that I've ingested from them.