Good post, Chris. It's much better to ask a lot of questions before handing over the money. My first thought concerning your post, are you sure Idaho is so backward that it doesn't have similar emission laws as California?
It's sort of true, no money --- no build! You're doing well, though. I suggest building in stages after developing a well thought-out plan with plenty of input from someone who's actively in the trade of building 4x4's! The first step is to learn what is necessary to achieve your final goal,sprung-over with 35's and lockers. There are a few articles at 4x4wire that discuss doing exactly what you want to do to your YJ. This would be a good beginning.
I wouldn't begin pulling parts from the boneyard until I had developed a real doable plan with a 4x4 builder.
Idaho isn't exactly a 4-wheeling "Mecca", however, I'm sure there are several interesting trails there for hardcore four wheelers. More than likely, what you're building there for California four wheeling venues will be way over built for Idaho, except for the short block engine.
With a good plan, building in stages, your built Jeep should be much less than the cost of a Rubicon. But,the project you have outlined above is going to run at least $10,000 in parts, even considering the fact that you're going to scavenge the boneyards for as many parts as is possible. That's just a guess, could cost you a lot more to do a complete bug-free sprungover Jeep w/ a shortblock.
A built Jeep IMHO is much better than a new Rubicon, one thing's for sure, you'll not have to fret over dents and scratches in your old YJ. Yes sir! you've pick a fine hobby, empty-pockets! <img src="/forums/images/graemlins/lol.gif" alt="" />