I can tell you the steps I've taken just to give you an idea where you
might be headed...
I had a 3.5" lift put in my 1998 XJ (mostly the same as you 2001) and also experienced drive-line vibes.
1) Dropped transfer case 1"; Vibes were a little better around town but still bad on the highway.
2) Tried a 2° shim on the rear to bring up the pinion a bit; again, vibes better but still bad.
3) Ponyed up the cash and got a Tom Wood's SYE (slip yoke eliminator) kit with custom driveshaft (not hack and tap); No vibration at all... till about 65mph. The higher speed vibes were due to incorrect pinion angle, the 2° shims were not enough.
4) Ordered 6° shims... 4° shims arrived in the mail
. Since I had them thought I'd give them a try.... Vibes gone.... till about 85 mph, them minor but present, under load.
5) 6° shims installed and transfer case put back in stock location. Finally Fixed... Correctly! NO Vibration! :yelclap:
A side note...
The Tom Wood's kit I got is known for leaking oil out the seal at the transfer case output shaft. This is because the seal - press fit - is not tight enough. The instructions recommend sealant of some sort, others have tried other sealants and glues with varying success. I just had my Xfer case tail cone replaced with one machined for a good seal fit.
I just looked at
Tom Wood's Custom Drive Shafts site and noticed they now carry a tail cone by Advance Adapters, so the oil leak may not be a problem any more.
Good Luck