Good advice from both, but I'd start with checking the U-joints. IMHO a 3" lift should not give you vibration problems, esp not with a relatively new TJ. Next I'd be checking steering components and alignment unless I was sure it was caused by the drivetrain.

97tj, Shaved Ford 9 rear, 4:10's, New 35x12.5 BFG KM2's to test!, Warn x8000i, ARB's, Quick Disco's, Hand Throttle, & it's my DD. smile