installed rough country 4" lift and now you can visibly see that the upper ball joints are 1 to 2 inches behind the lower.
Called R/C and the lower control arms are the correct length 17.5.
Any ideas would be appreciated.

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Take a pic of the front driveline, shaft and pinion in frame.

not the best shot

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Pinion does indeed seem low. You'll need to shorten the lowers. Or extend the uppers. If they're fixed length arms, you'll need to mess with the cam bolts. If no cam bolts, you're stuck without adjustables. I would not cheap out and get cam bolts, unless you can find someone's takeoffs for no charge just as an experiment.

Have you driven at highway speed to determine if you have vibration and/or lack of steering stability? **edit: With a low pinion, you'd have extra caster and no stability trouble, but maybe sluggish steering. But likely shaft vibes.

You're driving what model and year?

This is where an angle finder comes in handy, btw.

NO, you always set to caster angle NOT to be aligned to be paralleled to shaft on the front. Remember this is NO load 2x4 on the street. off road speed are generally to low to cause an issue.

You need to measure your caster angle. Use a angle finder app for your phone. If its around 4.5 you are good. IF and only IF it does vib. dial in less caster but only what it takes.

If you just dial that up to be parallel you will end up with ZERO caster. this will make it handle like fecal matter and make it darty as hell.

My jkr has 4.5 lift and the angle is about what you have from what i can see.

Issue will happen IF you gear to low. remember these drive shafts have a RPM limit when set up like we do. I run 4.1 have no issues. If i ever gear to say 4.88+ it very wellbe an issue. at this point you have few choices and NONE are low cost. you can get locking hubs kits. You can get a cuton axle with the Cs clocked to the total angle of caster +drive shaft angle.

its a jeep thing......................................

I disagree. Caster is nice, but eliminating vibes is required. Vibes can and will ruin seals and eventually bearings. No load vs load matters not, it's simply rotation. Even worse that this is on the street, that's where higher shaft rpm occurs. 2x4? Why are we discussing a front driveshaft then?

The pinion angle always (!) takes precedence over caster angle. Always always always. Run as much caster as you can until the front u-joint starts vibrating then back the caster off until the vibration is completely gone.

yes but he needs to know where he is not guess( looks likes two inches back is what he said). 2" rotated forward would be so far off it will never steer well.

set it parallel at 4.5 lift whats your caster numbers? 0 maybe 1. try to find a happy place. if zero is all you can do that wont be a good street set up with zero caster, wont return to center and can help in the DW issues***. Like i just had said My jk has 4.5 lift and i have 4.5 ish of caster. no vibes up to about 90mph. then it will start to vib<<<reached its RPM limit in a NO LOAD. No if jumped from 4.1 gears to say 4.88+s that speed where it happens then would be about at a much lower to speed. as those gear get deeper this issue just gets worse
*** so what you going to do then? nothing except reclock the Cs or get spin teck hubs.

carry on...you seem to have it under control.........

Your JK does not require as much caster as a TJ does and 4.5 degrees is not enough for a TJ. Even with 35" tires that requires less caster angle for good steering traits than a smaller tire. For a TJ a bare minimum of 5.5 degrees is recommended with as close to 6 as possible.

still going to be rather hard to be at 4" an up and have both angles correct if its a drive shaft rpm limit issue. Op is wj from what his sig claims.

but this is getting circular at this point. The op might figure it out. But i still see no caster angle given here just its 2" back. like i said for free any phone today can be a rather nifty angle finder. dont guess measure it. this is getting like shocks........... or what size tire