Picked up a 2000 XJ last week with a 4.5 inch lift and 1 inch spacers up front and 1 inch blocks on the rear...yea I know not a good idea. Any way when I got it ...it had really bad vibrations. I took off the front drive shaft so see if that would help but no luck. The XJ already has an SYE installed. It also had a transfer case drop. How can I check for bad U-joints? Should I reinstall the front drive shaft and take off the rear and see how it runs? Any one experience this? The jeep was neglected for a while before I picked up.

I was told you need to get rid of the TC drop when you put in a SYE. That's what I did when I installed my SYE, Might start there. After I got rid of the TCD I had to get 4-5 degree sims for the rear axle. Mines a 2000 at 4.5" lift with no vibes.

And sure, take off the back shaft run the front and see if the vibes are gone. Dont hurt to try and diagnose it with a small test right?
At least then you will know for sure its the driveline and not tires or whatever.

Ditch the tcase drop.

I'll take it off tomorrow or the weekend . ill see how it rides. Didn't think it would've been such a big deal with the TC since it has the SYE

They are both correct, and my 99 with an SYE has shims also.