I just rebuilt my 2000 4.0. When driving i get this low pitch whine starting about 2k rpms. The noise is not present lower then 2k rpms. It is also not noticeable when the jeep is in neutral at any rpm range.
I read that you really cant put the flywheel on the wrong way. The only thing im not sure about is the shim with the flywheel. i can't find any pics that show its relation to the flywheel.
When is put the flywheel on. It went stainless flat plate thing. Flywheel. Shim. Then bolts. Torqued 105 lbs.

 

I've got the same thing going on.Mine sounds like im dragging a tin can down the road. I had to yank the transmission out to change a seal, only 2 bolts were holding the tranny and motor together.I fixed all the presidentail solutions that some moron did to the Xj and now i have this going on....

 

Does the noise change pitch when on/off the gas? If so could be a pinion and or carrier bearing. FWIW seems like any shims would be placed between the flexplate and the crank.

 

The pitch does change on and off the gas. It doesn't get louder with the rpms. Its just present. Its just barely been over 3k rpms though and medium throttle. The motor only has like 600 miles on it. It does make that whine from 2k-3k. fluctuating slightly with the gas.

I did have a slight bit of difficulty getting the motor and trans together. Could i have messed something up on install?

As far as the shim. Maybe its in the wrong spot. i was almost positive it went on the transmission side of the flywheel. Hopefully someone can clarify.

There is also a 2inch thin metal band going around the flywheel. When i had the motor out and was installing the flywheel. i was using the slots in the rim for leverage with a screwdriver when i was tightening the flywheel bolts. Maybe i bent it a little bit.

 

Ouch. Those slots are used to cause pluses in the crankshaft position sensor. Critical.

 

Gotta love learning stuff the hard way.

 

Pic of a flexplate installed showing the flexplate backing plate [shim] in place.

 

Thanks for the pic. Guess its time to take the motor and transmission apart again. But from the transmission side. It won't be too long before I've touched every bolt on this thing.
I'll need to do some research on how to tighten the flywheel bolts.

 

Let us know what the problem was..