Do you want a mud rig, or a trail rig? The two are not one in the same. Take a good hard look at what you use your Jeep for now, and what you will use it for in the future.
Your 2012 has the Pentastar, right? I don't know how much support there is in the way of supercharger kits for those yet...and according to the people that I know who own them , the Pentastar is god's gift to Jeeps, right?
Also understand that the more HP you add, the more money you will spend. Either on upgrading driveline parts, or replacing driveline parts.
For a lift, I'd buy something that uses top-quality joints. I don't believe that BDS qualifies. I don't know a single person that's purchased a Currie or Clayton lift and then regretted it. For a JK-specific long arm, Clayton makes a kit that's radius arm front, 4 link rear, and Off Road Evolution makes a kit that's 4 link front and rear. Here's my question to you....WHY do you want a long arm lift? Not that there's anything wrong with them....but don't go long arm for 4.5 inches on a JK just because someone told you that long arms are way cool.
For your front axle, since you have to buy a D44 to go in there anyways I would probably just buy an axle that is suitable for your intended purpose. If you buy the right D44, you won't need to sleeve it. Don't forget your rear axle either - depending on how you're going to wheel, cromo shafts may be an idea.
Why do you want to run 5.38's with 37's? That's shallower gearing than the stock Rubicon (4.10's with 32's). Have you figured out where your engine would be revving at 120 KPH on the highway? Speaking of gearing, are you looking for a 2 speed or 4 speed Atlas? What sort of ratios?
Armor - are you talking about bolt-on sliders and bumpers, or an exo-cage? If you want to build your rig to be amored up so that it can take anything, you had better have deep pockets because no amount of armor will be enough to deal with careless and/or unskilled driving on the trail.
What about the stuff you haven't mentioned? I think that it would be foolish to dump a huge amount of money into a rig and not include quality beadlocks in your build plan. If you're buildign a really wild rig, at the very least you should probably beef up the existing "cage".