Just installed the 2" lift and had alignment done. Rides good, a little more body roll than before. I am not getting any driveline vibes except when I take off (I have the 6 speed manual, 2006 WranglerX) the Jeep wants to shake back and forth. The stick will rock from left to right till you get going then everything is ok. Just an awkward feeling as it rocks the cab left to right as well. Any ideas what it could be. It just doesn't feel solid like it did before it was raised.  

Have you put taller tires on it?  I put tires on mine and got the shaking shifter.  Turned out to be clutch chatter. I let the clutch slip a bit while taking off and it doesn't do it any more.  

also check to make sure your tires are ballenced right. You can also add a adjustable front track bar. and HD steering stabilizer.