Everything on the factory jk is weak regarding suspension, axles, steering etc. In my opinion. My JKRU weighed 5500lbs with myself in the seat, full tank of gas and one tool bag. On many trips I'd say I was well over 6k lbs. Some trips with four adults and the rear stacked to the roof with gear (and a hitch rack with cooler etc), and a 5 week trip with my wife and I, lots of gear, thousand of miles, hundreds off road. The AEV suspension made a huge difference in handling, off road and on. I also put a ton of money into steering components, all upgraded ball joints, tie rod, drag link, track bars etc. The front axle was trussed and gusseted. D rated 35" tires. Eventually upgraded control arms, drive shafts, teraflex HD 44 front axle. On and on. Because the factory pieces were quickly wearing out under my use. I also re-geared the axles, some configurations are very poorly geared.
When all was said and done it handled very well, even fully loaded. But it took a lot to get it there and make me feel good about using it hard in remote places.
Brian, got any more pics of the jeep from the front or angled?

Your build and mine are pretty similar as far as some of your more noticible choices. Here's a quick list of what should be here by weeks end:
JE Reel 1350 CV front drive shaft (here)
JE Reel 1350 CV rear drive shaft (here)
Dynatrac ProRock 44 unlimited front axle (4.88)
ARB 35 spline locker
RCV Ultimate axles
Reid Racing knuckles
Dynatrac pro steer ball joints
Dynatrac ProRock 60 rear axle (4.88)
ARB 35 spline locker
Hutchinson Rock Monster Beadlocks-black (here)
37" BFG KM2s
Synergy track bar relocation brackets, welded...both axles.
Synergy HD tie rod
Synergy Sector Shaft brace kit
Synergy HD Draglink w flip kit
Metalcloak HD adjustable track bars...front and rear
Expedition One trail series front bumper (customized)
Expedition One Rubi E-Disco skid
Expedition One trail series rear bumper (awaiting the gen 3 revision to ship these three)
Warn Zeon 10-s Platinum (here)
The lift itself is sort of a frankenlift:
AEV 4.5" RS Tuned Bilstein 5160 reservoir shocks (here)
AEV 4.5" progressive Springs (here)
Clayton long arm kit custom made with MetalCloak DF joints
Clayton HD crossmember, welded in.
Clayton trans/oil skid...might do the other two as well.
Clayton LCA skids
Probably going to look a lot like your rig from the front!
As far as the weight issue, it seems like the general consensus is that issues regarding payload are directly addressed with upgraded suspension components, lower gearing and axle/axle end reinforcement or upgrades? If so, than I'm going to call it a day and say no worries...