I installed a new clutch disc, pressure plate, throwout bearing, and pilot bearing (what you are referring to as input shaft bearing). It also did not make any difference. I'm quite convinced it's some sort of harmonic vibration that only exhibits itself in the manual without a torque converter. One of these days I'd also like to get an HP tuners and compare the maps of different years and transmissions to see if any of the stock tuning could be causing the noise.I have experienced the exact same thing since I purchased the jeep a year ago. I have the 6 speed so it certainly seems to be an issue with the 4.0/NSG combo. From what I was told by my local transmission shop, it could possibly be a warn input shaft bearing. Id like to replace that and go from there. Mine seems to get slightly louder after long drives. I have a 2 hour drive between home and school. On the occasion I make that drive, the noise is certainly more noticeable when downshifting on an exit ramp.