Be mindful, as I am sure you are, of the gearing you plan on using. I had an '01 TJ for 5 years, loved it, but I know as torqey as that motor was it will be nothing like the 4BT will be, even stock, much less a built one.
Back to the gearing. Personally, since you will be doing freeway as well as off roads, and I am sure MPG goals are part of that (mine got 15 MPG highway) I would not go lower than 3.73 ratio. Any lower and it will be a rock crawler only. I am sure 4.10's will be drivable, but if you get up to 65 the RPM's will eat your gas. As I said, I am probably preaching to the choir here, but just thought I'd throw it out there.
Plus the taller gears (3.42 or 3.73 vs. 4.10) will be stronger, since there is less teeth per gear, thus more metal on the teeth.
Also I noticed on the intercooling plumbing, the top tube, on right hand side (in the pic) looked like it had a pretty decent size kink in the bottom of it. Big restriction. Or was that a mock up?