2000 Jeep Wrangler Strange Whining noise

Sounds more like the pilot was knocked out when the trans was installed. DId you get a junk yard trans? did you use the proper oil in it? Make the noise regardless of what gear it is in?

Thats what I was afraid of! yes the tranny was a junkyard one. Yes the proper fluids were used. Guess I need to pull it back out and check it...and replace the pilot if needed. Thanks.

Let me know what you find in there

Got the tranny off this week. Sure enough the pilot bearing had been knocked out. Bought a new one, installed it and put the tranny back in. Now a new problem has arisen.....the car wont go into gear. I engage the clutch and all gears are difficult to go into and reverse is absolutly impossible.

Hate to say it, but sounds like the clutch disc got bent when reinstalling the trans or when you tightened down the pressure plate.The plate must be tightened down a little bit at a time, in a crossing pattern. When plugging in the gear box, the trans must never be forced in or left hanging until tightened up, this bends the disc and then they dont go into gear

OK...the tranny was fully supported until all bolts were torqued to specsand the transfer case was bolted on and the remaining supports were installed. Before I removed the tranny to check and change the pilot bearing, I noticed a vibration that got slightly more noticeable just before the tranny was removed. Also, looking back, the shifting got slightly stiffer before I rmoved the tranny. Could the pilot bearing being popped out and the vehicle driven cause a warping of the pressure plate? I'm just trying to figure out how this could have happened. The clutch set is only 8 weeks old! Should I replace the whole sytem (minus the pilot) or just the pressure plate?

Hard to say without being able to spin the disc to see if it has a warp in it, usually the disc and not the pressure plate that is the problem.Sometimes if th einput shaft can move around (no pilot) then it damages the disc. Does the pedal have a little free-play in it before you feel the clutch? I think I would try a new plate and disc, just to be sure,pulling a 4x4 trans isnt the funnest thing in the world

To be sure it isn't fun! Seems I'm getting pretty good at it though. All parts are now ordered and I'm just wiating for them now. Hopefully this ends the nightmare once and for all! Thanks for your help!

Just to give you an update,
I replaced the clutch, slave cylinder (I discovered a leak) and bled the system. Bad new is the jeep still won't go into gear! When the engine is running and I depress the clutch pedal, I can hear a slight whining in the bell housing. Could it be that the slave cylinder isn't pushing the clutch fork forward enough so that the throwout bearing (also new) isn't engaging the cluth properly? I looked and can't find and adjustment to the pedal. I'm at a loss now!