You've pretty much got things figured out.
The biggest question is whether or not you do or do NOT have adjustable control arms & track bar.
If you DO NOT have adjustable control arms for all 8 arms, you're wasting your time until you get some.
You seem as though you've gotten this far in what you know, so i'll assume you've already taken that into account and you DO have adjustable arms as well as adjustable track bars.
That the trackbar centers the axle side to side.
So far I disconnected the trackbar, took springs out and brought the front axle to full bump... the side to side position of the bumps are way off.
You answered your own issue with this statement. Your track bar is what determines your side to side position.
With the track-bar removed, there's absolutely nothing in place to keep the axle from shifting side to side.
As long as the axles aren't so far off as to cause issues during the rest of the alignment process, I wouldn't worry about it, as you can re-center when you replace your track bar.
The track bar NEEDS to be set at ride height, because setting it now at full bump will equal un-even axle placement once you drop the axle back down to ride height.
(but again, if it's completely OFF the bumpstops, you might want to reinstall the track bar just to keep you in the general ballpark in relation to your other arms binding, or use a strap connected to something secure to hold your axle in place)
From what I read you just adjust the second upper control arm to fit once you set pinion angle - we are not there yet.
At full bump with no springs, you should remove all upper arms, as they'll just cause binding issues in regards to setting your lower arms.
Keep ONLY the two lower arms attached. Pinion angle will be situated at a later time, at ride height.
Don't worry about the axle rotating. If you've got the axle smushed against the bumpstops, the pressure of the jack & contact of the bumpstops will keep it from rotating.
With only the two lower arms connected, spin them in/out until you're centered on your bumpstops.
When I got to this point, I took my tape measure and measured from the axle tube to somewhere solid on the frame (like the skid-plate mounting bolts)
This way you can determine that both lower arms are correctly adjusted, and the axle is 'square' in relation to the frame.
IF you find that one lower arm needs to be slightly different than the other, that is fine. As long as the axle is square to the frame.
Once you've determined that your lowers are correct, DON'T tighten anything. Just snug them up so that they're 'mounted' but can still allow the axle to freely move. (tightening all the bolts will be the absolute last step)
Re-attach the driver side upper arm at the differential mount (again, don't tighten it, just snug it enough to stay put), and keep the passenger upper OFF the Jeep.
Reinstall your track bar, your springs, and your tires. Then set the Jeep down on its own weight.
At this point, you can crawl underneath the Jeep and set your pinion angle.
(since the lower arms were determined previously, the axle physically cannot shift from it's position, but it CAN still rotate.)
If you've got Double Adjustable arms, this can be done with no additional tools.
If you've got Single Adjustable Upper arms, you'll need to place a jack underneath the front pinion to remove tension on the Upper Arm.
Make sure to do this part safely, and use your brain/judgement well.
Spin the upper arm until you've got the pinion angle you desire (within a few degrees. You might need to fine tune this after everything is done).
There's a few good threads on this forum regarding proper pinion angle.
For a starting point, it's typical to match the front pinion angle directly to driveshaft angle.
Once that is set, install the passenger side upper arm.
If you've used a Jack underneath the pinion to relieve pressure, remove it before installing the final upper control arm.
Do NOT blindly set the Passenger Upper to the same length as the Driver Upper.
It's likely (and common) that the arms will have different lengths. Mine were 1/2" difference.
Completely disregard your Driver Side arm, and mount the passenger upper in whatever length that the bolts easily slide into the holes.
Don't force anything to move or shift. Just spin the arm until the bolts go in easily without coercion.
After all of this is handled, you can then adjust your front track bar (again, at vehicle-weight ride height) to center your front axle.
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I need to note, in my experience of doing this a few weeks ago, it is likely that these will NOT be final adjustments.
After getting everything dialed in, I removed my springs and cycled my axles to full-bump again. Checking for any interference/unwanted contact.
Hopefully you will have none, but in the event that you do you may need to lengthen/shorten your lower arms to allow clearance.
If you change the lower arm limits, start back over at that point, and re-adjust everything one at a time again.
(I think it's pretty self-explanatory to note that the lower arms should be adjusted the equally. ie; 1 turn on driver side per 1 turn on passenger side)
Once you're satisfied, torque everything to spec.
I personally went around underneath and torqued everything twice, just to make sure I didn't accidentally forget to torque anything.
(loose control arm bolts can present themselves in a few 'wonky' & weird ways)
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I'd suggest giving this thread a good read, and even follow along with it as you perform your work.
https://wranglertjforum.com/threads...-control-arms-on-a-jeep-wrangler-tj-lj.17062/
