My question was "Did you remove your t-case lowering kit after the SYE?"
After re-reading your original post ("put the drivetrain back where it should have been..."), I take it that you removed the t-case lowering kit.
The Jeep had all that on (lift, t-case kit, SYE, CV drive shaft) when I bought it. My rear drive shaft is practically a straight line. Looks to me as if the t-case kit is not necessary.
JimG