So here's the deal. A couple of months ago I noticed a problem with my transfer case. Once I confirmed the problem I removed the front drive shaft, front output bearing problem. I drove for about a month, tops, without the front drive shaft.
I got a replacement TC and had it installed the other day, no more noise from the transfer case, but now I have another drive-line noise.
It's a whirring noise during acceleration, and sounds like it's coming from the front of the foot well.

My question is could running my xj without a front driveshaft have damaged the front differential at all? Caused the front pinion bearings or carrier bearings to go bad?
This is a brand new noise, it wasn't there before I removed the driveshaft, or while I was running without it. It only showed up once the new TC was installed and the driveshaft reinstalled.
There doesn't seem to be any play in the front driveshaft to the pinion. No noise when you spin the front axel, or driveshaft by hand. All bolts and connections tight. I just changed the diff fluid about 2 months ago, put in Lucas 75-90W, and it's fully topped off.

Additional info about the jeep
4.5" RC lift
No mods to the TC or drive shaft, just the 1" drop that comes with the lift kit.
New U joints on the front driveshaft, and front axel.
New bearing hubs on front.

 

Could a u-joint have been improperly installed & damaged? That's what they did to my Cherokee.

 

I installed all the u joints before taking off the driveshaft. Everything ran fine while the driveshaft was off. All joints where checked before it was reinstalled.

More info about the noise.
It is most noticeable between 15-25mph around 2k rpms. It increases in pitch as I accelerate through those speeds.

 

"I installed all the u joints before taking off the drive shaft" What? oh I see you must be.



Just messing with you..lol

 

New transfer case new noise seems pretty straight forward.

 

That was my thought, which is why I went right back to the shop with it and had them take a look. Everything is tight, there is no noise coming from anything in the TC. When you are in the Jeep driving it and hearing the noise it sounds like it's coming from the front right side of the drivers footwell. It doesn't sound like it's coming from the TC.
Are there bearings that could have gotten messed up in the transmission when a transfer case is installed? I thought it was a pretty straight forward, output shaft slides into transfer case, bolt two together.

I'm still wondering if it's the pinion bearings making the noise now that the front driveshaft is connected again, so there is weight on the front yoke again.