I'm in the process of doing an SYE on my Cherokee. I'm wondering how you adjust the pinion angle. I read something about control arms at one point, but I'm not sure if you just shim it or what the best way to do it is.

Any opinions greatly appreciated.

Since you mentioned the SYE I'm going to assume you mean the rear. To adjust that you are correct and need shims.

To adjust the front, you would have to adjust the control arms. Unless you did a coil conversion in the back, your XJ should have leaf springs and will not have rear CA's

That's why I was confused. How do I know which shims I need and where can I get them?

Use an angle finder (there's an app for that) find out difference between drive shaft and pinion.
Should be the same +-1°.
Serious has them i believe, or iro.
Look for steel shims.

Thanks for the reply. I'm assuming it would be better to fix the lift in the rear before doing that? Would a slight difference in lift be a deal breaker on a particular shim?

Depending on your lift height you'll need a 2, 4 or 6° shim (I know those are the increments that RE makes their steel shims in)
I have an RE 3.5" lift and used a 4° shim and its near perfect.

YMMV obviously since even lifts from the same manufacturer settle at different heights.

Cool, thanks. So in theory the vehicle will need to be down long enough to get the SYE on, and measure what I'll need, then order and install the shims, right? I'm assuming you can't drive on the stock pinion angle with the CV shaft?

You can drive like that, going to have vibes.
I wouldn't do it for long tho.

You can. You'll get vibes and it could ruin a pinion bearing or worse if left for too long. Don't know how long too long is but it's obviously not ideal. Most people, myself included, toss in a 4* shim and call it good. 2, 4, 6 are the most popular ones. 8* get iffy and I wouldn't use it. You're too tall at that point anyways :P shackle angle will also change your pinion angle

Are you lifting also or just installing on stock height.

It's lifted already, but the back is on blocks. I'm going to get shackles and 3.5" leafs for it, but it's still in the prelim stages.

If you plan on getting new springs and shackles soon, I'd measure the pinion angle after the new components.

Not mentioned earlier, you can replace the leaf spring pads and re-weld new ones at the correct angle so that shims are not needed. This is a lot more work, but I believe it's worth it. At the same time, you can also move your rear lower shock mounts for the correct angle and move them so they don't hang below the axle.

Just food for thought.