Not aware of your tire size but, doesn't matter what the cups do if the tire hits the body.
1- set both lower arms the same length
2- install one upper and dial in approximate pinion angle
3- install trackbar and center axle side to side at ride height
4- install shocks so the travel up and down can be used to cycle the axle
5- cycle axle full articulation with a tire on the up side to check for clearances, trimming, bump stop adjustment for shocks at the same time or right before you put tire on.
6- after tire is on and articulated and any front to back adjustments have been factored in, then check the bumpstops against shock travel, how they line up, how much extra is or isn't needed.
7- fine tune pinion angle with the single upper and both lowers. Only after all else is done does the last upper get installed.
It isn't a defined step by step do this then that process. Each adjustment affects other things so the whole mess needs to be evaluated for what is going on as you dial it in.
I see what you're saying now. It's an overall pain in the dick doing it for the first time, but I get how it needs to end up & what all the different inputs do, so I'm figuring it out.
I got the axle centered longitudinally, with 33s I discovered that I rub with the Sahara fenders about 2" before bump stop - dunno if the wife will be good with getting rid of the fiberglass fenders, we'll see.
I installed the springs, connected the TB, put it on the ground, saw that the axle was about 1.75" off to the right, so I put it back up, removed the springs, drooped the axle until I could get the axle end of the TB out & adjust it as necessary. It's centered now.
Wasn't sure if it was safe to have both uppers removed with weight on wheels, so I jacked it up, removed the springs, supported the frame, set the axle at ride height, & set the pinion angle so the rear yoke points to the SYE yoke. Re-installed everything & it stayed put. Called TW with driveshaft measurements, should be able to pick that thing up on the way home tomorrow.
If you told me a few months ago that I had to pull the springs on a TJ I'd block off a few hours. Now I know I can do it in 10 minutes.
At least it’s on it own weight at this point