Is there an inspection cover on the bottom of the bellhousing??? If so, you can remove it and check to see if there's any pieces of the disc laying in the pan, or visibly missing from the disc..... you can rotate the engine with a socket and breaker bar on the crank bolt and with a good inspection light you should be able to see at least the outer portion of the disc....

Could also be the throwout bearing starting to self destruct.... While you're under there, have someone push the clutch pedal in and watch inside to see if things are working correctly....

I've had diaphragm clutches break a finger sometimes and make a similar vibration, no idea what kind of clutch your jeep has......

As for the grinding on shifts, could be something as simple as the adjustment.... might want to check a service manual for specific adjustment procedures on your jeep.