Been so impressed with the Synergy springs (after RK & EVO) on the JK that (for the new JKU) I am hesitant to try anything else. Metalcloak is intriguing but I am not sure if their springs are stiffer or softer or what.
Can't speak for the new RK joints (I had the regular ones) but the ROKMEN Johnny Joint arms were a bit more comfortable and still tight-feeling. So if I had to do it all over (and I soon will) I'd go Synergy springs (with MC as a second option) and ROKMEN or Metalcloak arms. Shocks- probably the Bilstein 5100 (tried RK RRD, ELKA, and Old Man Emu) though the ELKAs were pretty decent and soft (expensive though).
The main issue I would try to avoid is drivetrain vibrations after the lift. With a short-arm system, nothing improves the ride more than the AEV (Rancho makes some too) drop brackets...nothing. You give up some CA bracket clearance though. So you can reuse some or all of the stock CAs if you do that. If you are not bashing the heck out of your CAs and not running really hard trails, the stock arms are extremely comfy and durable. They just don't flex as much. Lots of guys are starting to reuse stock CAs and the drop brackets here. It is also a cheap way to go, till you find you you really want/need more.
You can simply throw on some Synergy 3" springs (2" springs on a 2-door) or similar 2.5" springs, new shocks, and reuse the stock CAs with the AEV brackets. With flat fender, and 35s, even the Synergy 2" springs will work and would probably be my choice. Watch some of the competitors 2.5" springs. They will give you 4"+ on a 2-door, especially unless the JK is heavy. The RK springs raised my front by over 4". Not doing that again. On a 2-door, their 1.5" should work with flatties.
I just remembered your budget and the fact that this is a DD. Not sure if 2 or 4 door (this is important for spring selection) but here it is:
Bilstein 5100s (Rancho 9000s second choice and they are cheaper right now)
Synergy 2" (or MAYBE 3" but talk to them) springs
AEV Drop Brackets
Resuse stock control arms- nothing will last longer for a DD and I doubt be as comfy on the road. Plus, it saves you $1,000 easily.
Brakes- use 2 inch longer stainless lines (most are too long- look at Crown custom sizes) and Black Magic brake pads (way better than EBC). They will stop your 35s a lot faster. All you need are the pads or pads/rotors if your rotors are a bit old.