My 2001 Sahara 4.0L 5 spd has been making this noise on occasion. I took it to a clutch place and was told it was not the clutch. I then took it to Jeep and they said it was the input shaft bearing. They said they could replace it for ~$1000 or leave it alone and it would be OK. Now I am having more difficulty shifting. Does anyone know if the clutch is going or is this input shaft bearing finally going south for good???

Clutch pedal down--transmission is not turning--if you have noise--the clutch is not releasing or the pilot/throwout brgs are bad. With trans in neutral and pedal out--input and countershaft are turning--if you have noise the input/mainshaft pilot/countershaft brgs are bad. In fourth gear pedal out--if you have noise--input brg is bad--if noise is just lower then rebrg the entire trans. But that's just my $.02

I appreciate your response. So, you are saying to rebuild the entire transmission? I am getting noise with clutch in and out.