The steps I would take:
(Pull springs at any point before step 3)
1. Get the belly at it’s final height (Tucked)
2. Install the SYE and driveshaft
3. Lengthen the upper arms until your pinion is approx in line with the TC at ride height (using the jack stand to get there)
4. Shorten the lower slightly if your diff hits the gas tank, then shorten the upper until the driveshaft angle is correct again. Lengthen both if you still have plenty of room.
5. Check full bump and side to side bump to make sure nothing hits, if you need to lengthen lowers, you’ll most likely want to lengthen uppers as well and vice versa. Add or subtract bumpstop as needed to prevent damage.
6. At this point the axle should be as far back as possible without hitting anything through the suspension travel, with the pinion pointed right at the TC output.
7. Reinstall springs, and check driveshaft angle again to make sure your ride height was correct when you were setting it up.
8. (Optional) Meet up with me and have me reweld the upper spring buckets to get rid of the bowed rear coil spring
The benefit of pushing the axle back as far as it can go without interference at full bump is that when the Jeep is at ride height the axles come forward, the farther back you can push it without contact, the more centered in the wheel well it will be at ride height.
Also added note - trim the spring buckets to make sure the shocks don’t get wrecked, rotating the pinion up for the tummy tuck will make them hit at droop.