2001 Jeep Wrangler, 4.0, NV3550 5sp Manual, NP231, 80k. So i made a 300 mile trip recently and when i got up in the a.m. i noticed a constant knocking/rattling noise coming from from my bell housing area. It appears in every gear 2 or 4 wheel drive, hi or low when clutch is engaged and when you disengage the clutch it goes away. I checked both the trans and transfer case fluid, both clean and full with no obvious signs of metal fillings. Did a thorough inspection of u joints, drive shafts etc. No issues noted. So i drove it back home thinking that it may be a bad damper spring, marcel or broken rivet or generally clutch related. Removed the trans and pulled the clutch. Pilot bearing was good, flywheel was tight and no scoring or cracking that i could see but i didn't have it resurfaced or check run-out, the release bearing bad, it had play and bearing was a little noisy, no obvious broken parts on pressure plate and disk looked good, honestly i didn't check for end play on the input shaft of trans(boink on head). So, I scuffed the flywheel with 180 grit and put a new clutch in since i had it out (but at this point i really didn't think i solved the problem based on what i found). Took it for a test drive and same noise, came back and put it up on jack stands and there is no noise on jack stands at all, listened with stethoscope but nothing. So i pulled the rear drive shaft that has no play, inspected the yoke for the diff and transfer case and no play, went for a ride in 4 hi with rear drive shaft out (Slip yoke eliminator) and no noise. At this point I look at my u joints again and there tight, but it has been a few years since i rebuilt my Double cardan, so i put new spicer 1310x ujoints in, not convinced this is the problem. Put dshaft back in and same noise. So do you think i have a bad main or coutershaft shaft bearing because since i removed he rear drive shaft and took away the extra load of the rear drive train and there was no noise. Sorry for the long post but i want to make sure i don't overlook anything before i have to tear into the tranny. thanks for your valuable time.