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...I also drove around without the rear shaft and no clunking and no vibration.


Did you loose any fluid out of the T-case. If not, it may be empty ...suggest you check that too.

'89 Raider V6, AT, SAS'ed, Dana 44 front & rear, 5:38 gears, NP 231 T-case.
'97 Montero SR, cold weather package, 4.90 R&P, BATTLEZ suspension w/ 2" lift, JAOS grill guard & under body protection, custom rock sliders.