The only "non-Rubicon" change that I'm aware of with regards to drivetrain in 2000+ Jeeps is the 5 speed NV3550 added in 2000, the 4 speed auto added in 2003 and the rear disk brakes added in 2003. None of these should have any effect on the standard suspension lifts. For lifts like the RE long arm and the Skyjacker long arm, I'd recommend verifying crossmember fitment before buying...