Decide on a tire size and whether you want to run stock or flat fenders. With that info you can settle on a lift height. And from there, it really depends on what you want to use your JK for which lift you go with.
I've run 37's with flat fenders and a budget boost (took some trimming in the rear at the pinch seam). I've run both 35's and 37's with simple 2.5 inch lifts. I'm currently running coilovers set to about 3 inches of lift with 37's.
I get between 15 and 18 mpg in my 2012 with 37's. MPG is more tied to lift height than anything else. Same lift, with 35's, I got roughly the same MPG. Higher the lift, lower the MPG is a good solid rule of thumb.
If you settle on a budget boost, buy the cheapest you can find. They are all basically the same. You can run 33's with no chance of rubbing with a simple budget boost. 35's can be run with extended bumpstops. 37's can be run with flat fenders, a lot of trimming, and extended bumpstops.
From there, you're going to find tons and tons of options. Rock Krawler (despite the name), makes some excellent 2.5 inch lifts that work great for expedition type wheeling ranging from a basic spring lift to a mid-arm kit, to a full three link conversion that flexes like crazy. Personally, I'm not fond of their spring rates, but that's more personal choice than anything else (and it's actuall a statement I'd make about teraflex, rubicon express, pro comp, and most other lift manufacturers).
Teraflex also makes a ton of different lifts though I'm not at all fond of their control arms as I've blown out more of their bushings than I care to remember. I've also seen more than a few friends do the same. Hard to recommend one of their lifts based on that alone (assuming you actually intend to offroad your JK).
AEV is great, if you plan to stay primarily on the street or on easy trails. The brackets they use on their kits hang the body side mount of the control arm lower (which is great for geometry correction but terrible for ground clearance). Their lifts also don't flex to the same degree as those from Teraflex or Rock Krawler (in no small part due to their retention of the stock control arms). Again, which lift really depends on usage.
Personally? I'd go with a 3 inch Enforcer lift from Off Road Evolution. Run flat fenders if you want to run 37's. Run stock fenders if you want to stick with 33's or 35's (35's would be my personal choice if I was new and building a general all purpose rig that would see a lot of street miles). If you can afford it, spring for the King remote reservoir shocks (and if you can't, go with Rancho 9000's). Add in the EVO Draglink Flip Kit and you'll have a VERY solid kit that'll go anywhere you point your JK and will ride worlds better on the street. And if you want to upgrade control arms, I'd go with EVO, Currie, or Rokmen (by far, the best available today). I'm actually running the rear plushride springs from this kit on my JK presently (the 4 inch lift versions though given the weight of my JK it sits at about 3 to 3.5 inches higher than stock) and even my wife comments on how smooth my JK runs on the highway as compared to her Escalade.
Wheels? Take your pick. To beadlock or not to beadlock is not a question of DOT legality. Beadlocks are not illegal anywhere in the US and I challenge anyone to show me a statute that makes them so. It's simply urban legend that without the DOT sticker, they aren't legal on the street. I've run them on my daily driver for the last 3 years and have been pulled over in that time period in TX, CO, UT, NM, NV, OK, and AR and haven't gotten ticket number one. In fact, in most instances, the cop has asked if they were real beadlocks and then spent some time checking them out.
Go beadlocks only if you don't mind a bit of extra maintenance and intend to wheel in areas where airing down really matters. Otherwise stick with standard wheels. I have 2 JK's, mine runs beadlocks, my son's does not. We rarely run into instances where it matters.
What wheels to run is purely personal preference though keep in mind that lighter wheels (without sacrificing strength) have a lot of advantages and that generally lighter wheels are more expensive. Personally, I run AEV Pintlers on my daily driver and have a set of ATX slabs for pure off-roading, both are beadlocks (primary difference is the size of the lock ring, much larger on the ATX Slabs, and wheel strength, the ATX, though heavier, are substantially stronger). My other JK runs a set of inexpensive XD series wheels. Choose based on style and usage.
Tires? Wow, world of choices. Personally I'm fond of Nitto and Toyo, primarily because they have sidewalls that don't blow out and I tend to take my JK places that blow out sidewalls (I like to camp in out of the way places and see places that others have trouble getting to). I've also run the Goodyear MTR Kevlar's and while many hate them, I didn't have any bad experiences with them. Chose tires based on the type of terrain you'll be using your JK on. I run Nitto Trail Grappler's on both of mine presently and have no problem with them on the street and love them in the dirt.
