Check all drive line bolts. Check t-case mounting bolts. If still there, pull shafts and really check them out. Also you could pull the rear shaft only and see if the vibs still there as you drive slowly with just the front in 4h.
CJ.XJ.CJ. TJ. TJ.ZJ. TJ.TJ. ZJ.ZJ.YJ. XJ. JK
Also check your tranny mount. When you say it's not there when the clutch is in and then something pulled on your rig so hard that you dropped something out then you very well might've ravaged your tranny mount.
President - Arizona Off-Highway Vehicle Coalition
Vice-President - ASA4WDC
Arizona Rock Rats