I think your on a good path with carli. I have a 2011 2500 on a carli pintop, carli bjs, synergy steering, full leafs (sitting in the garage) and metal cloak control arms on order.
BLUF reccomendation: carli pintop, coils, bjs, trackbar, diff guard. Synergy steering. Full size spare (or 2)
Determine if you need arms. Determine if you need leafs. Determine if you need lighting
For suspension I think pintop will be fine for what you've stated. The bilstiens will be more once you factor in towers and I hear are better than the pintops when you get in the whoops. If you plan on hauling through the desert then maybe the bilstiens make sense. With my pintops my truck is happy doing 60mph through Forrest service and double track roads. I've hit 90 on the big open graded dirt roads with out realizing it. Where 2.65/3.0/3.5 shine is pounding through the desert. I would love to run the unchained kit but don't have the terrain to really use it. I barley put the 2.5s to work where I am but love the street ride they afford. The good about carli is that you can build as you go. The pintops and above have good resale value as well.
I would dump the money you save with pintops back into the front end. Good ball joints, track bar, and steering I think are a must. My steering tres were all shot within 20k. The new synergy setup is really sweet and beefy but I've heard they are having some distribution issues. If you want a steering RIGHT NOW give Strapt Performance a call. They have a pretty trick set up they can build but it's about 1k. Ball joints, carli or dynatrack.
Depending on what's clunking take a look at your control arms. I opted for metal cloak as theit dual durometer bushing intrigued me. If their claims are true, it should give the flex of a John join but the nvh of a bushing. As my dd this was important to me. It may be worth a look if you are doing long drives on your trips. Carli and thuren also offer some proven arms but I felt they were a little overkill for my set up. Synergy, thuren, and now carli (kinda) all offer long arms if it's something your interested in. If you do long arms, your shocks will need to be valved to it. Doing suspension right with a dodge is expensive.
I bought full leafs as they supposedly make some of the biggest difference in ride. I'm unloaded 90% of the time and when I tow, it's my rock crawler on a load leveling hitch. If I sag too much I'll get air bags and cradles. If you are running with 1k in the bed all the time, you could check out the heavy duty springs. This really is dictated by your load as already stated.
Lighting is something you may consider. I hated my lights and did a hid conversion which is ok. Once you get off the beaten path it gets really dark. If your looking at lights buy once cry once. I'd look at Baja Designs. I've run cheap 8in hids, cheap led bars and they are exactly what you pay for. My 30in in cjc brackets looks really cool but only throws usable light as far as my head lights. I don't know the answer to lighting but my first call will be to Strapt Performance or CJC Offroad when the funds allow.
Misc items to consider: front diff guard (carli or ruffstuff) is a cheap investment from a really bad day. Full size spare. It's going in the bed at 35s. Stick with a 17in rim and try to find a way to fit that in with your packing, if you can, depending on how far you go, 2 may be a good idea. Check out HRT Offroads build thread. They built an overland rig that the drove from Canada down to Baja Mexico and back.
Some of the builds on here are amazing. Building a full size dodge is fun, but expensive. My advice is to put the money into the components that will get you out and back safely first, and then look to the cool guy bedracks, rtts, and fridges.