I have a 93 YJ (manual) running standard axles with mild body and suspension lift on 33s. She performs beatifully both on and off road and remains to be the best car i have ever owned.

However i have just developed a problem which i think could be very expensive.

In neutral there is a very serious vibration which also feels like it may be dragging on the engine whilst idling. When the clutch goes down this dissapears and its as smooth as ever.
I thought that this was just the release bearings and was ready to buy a new clutch. There is no clutch slip and whilst driving there is no real problem till you let off the throttle. There is a clicking noise off throttle (using the engine to slow the vehicle) which sounds a bit like cogs jumping and i can only get it into 1st 3rd and 5th. I have checked clearance of the trannie tunnel to shifter and nothing has moved. Is the gearbox terminating itself?

Vague description i know, but i am hoping some of you jeep experts that could touch the paintwork and diagnose a problem, will make up for my extreme lack of experience..

I would really appreciate any thoughts.
Thanks