Your suspension lift is only 2" so you do not need to install a SYE kit and CV driveshaft. Those are only recommended for a TJ for a 4" or taller suspension lift.
Dropping a t-case an inch is commonly done with 2" to 3" suspension lifts to eliminate u-joint vibrations caused by 2" or taller suspension lifts. A t-case drop is not installed to cure a clunk which is caused by something like a loose bolt, bad u-joint, bad control arm bushing, bad transmission or motor mount, etc..
If your rear axle's control arms are stock, your rear axle's pinion angle and driveshaft angle are both fine.