When do you feel the vibrations? I have MT's and they are smooth at speeds greater than 5 mph.
If your Jeep has vibrations at speeds greater than you might need a transmission drop. In your lift kit should have been several 1" long spacers. Those are to put inbetween the transfer case skid plate and the frame. This will lower the transfer case and should eliminate the vibs. However, you may have a worn U joint in your rear driveshaft. If so this is a easy and cheap fix.
In the future you will want to consider a slip yoke eliminator and cv driveshaft. These two items will allow you to raise the transfer case back up to its original position and realy increase your rigs strength.
Hope all of this helps.