I figured I'd throw my hat in the ring here, in the process of swapping in a whole new drivetrain and on my list of items was the Savvy skid. I have NOT started the Jeep (obviously), but it looks like the top rib of the transmission bell housing does impact the fire wall as seen in the picture down below. Perhaps this is the source of the vibrations you guys are experiencing? Food for thought. I for one am going to massage that over with the mallet when I pull the engine tomorrow.
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For reference this is a 2004 LJ with the 4.0 and 42rle. Good luck boys!