We found the source of the vibration. When the tranny was separated from the engine, the pilot bearing hit the ground! Unbeknownst to us, there are two different pilot bushings used with the 4.0L: one large and one small. Our engine and tranny came from different vehicles, and the engine was originally in front of an automatic. We ordered what we thought was the correct bearing for the application, but we were wrong. The ID is the same, but the OD is different and determines the depth of the bearing in the crankshaft.