I just recently added a UCF Original extra clearance skid to my un-lifted TJ. I used UCF's Lo Pro mount along with a MML. "Had a 1" body lift on previously.
The drive shaft and u-joint angle was a bit much for my short TJ. I spaced the skid down temporarily with washers, the vibes diminished a little. I ended up ordering some Currie upper control arms and a Tom Woods Drive shaft. I installed the Arms first and adjusted them for the stock drive shaft; u-joint vibrations diminished surprisingly but not quite gone. The Tom Woods CV drive shaft went in this past weekend. I've been fiddling with the pinion angle (2*, 1*, 0*) to make it as smooth as possible.
Notice I didn't say smooth as stock. The UCF Lo Pro mount transmits a bit more engine vibes than stock and makes it's presence known. My suggestion: if you have vibes after the TT, get upper control arms first. You might be good with just that.