Sound very similar to what happened to my brother's XJ after a motor swap. There are 4 bolts that hold the bellhousing to the motor, the top two were in and a tad loose, the bottom left was gone and the bottom right was almost completely out. This causes where the motor and trans meet to start to pull apart, drop down, and makes both the starter and trans input shaft out of alignment. It will make it hard to start with a rattling sound, and make it damn near impossible to use the clutch. It also causes a good amount of damage to the clutch, trans, and starter if left that way. Check all 4 of those bolts and make sure they're nice and tight.
Also... just an FYI (and being a bit nit-picky), the Jeep 4.0 is not a V6. It is an inline 6.