I have a noise that sounds like a bearing growling and it really sounded like it was coming from the front so I did a front knuckle rebuild - much easier than I thought it would be, but the noise did not change 

It sounds like a growl/rumble; it is constant; it is speed dependent; it changes/is a little worse when I let off the gas; it is there when I have the clutch pushed in and when it is in neutral rolling down a hill; I can feel it in the floor; and it still sounds like it is coming from the front, but I read in one of the other posts about bearings that samurai's can throw sound all over the place.

In addition to the front knuckle rebuild, I have changed the U-joints with no change in the sound.

I am thinking that it may be the rear wheelbearings, but I am not sure how to rule anything else out in the rear axle, like a problem in the differential or how to tell if it is an input/output shaft on the tranny or transfer case.

One more thing, it is an 88 stocker with no drivetrain mods.  Thanks in advance for your help!

Wheel bearings sound like a rough old gravel paved road, easy way to listen for it
is to find a really new smooth road so the road noise is not a factor and drive/listen
for the problem.

Diff gears tend to whine, and change with speed, trans gears are noisy throttle on,
and generally quieter coasting no engine braking, your diagnosis sounded pretty good
except a little more noise when throttle is off, so unless you were in 4WD the noise
is going to be in the rear driveline, but wheel bearings will not change with throttle
changes, so I am thinking bearings in the trans, t-case, or rear diff gears/carrier bearings,
and being it's more noisy throttle off, I would start by draining the rear diff and look at
the magnet in the drain plug for any metal pieces, there should be a black paste that
is normal wear, but nothing like a shiny flake or small bits (sand size) metal.

NOTE: make sure you can get the fill plug out before draining the diff, or any other box/
case that fills thru a hole in the side before draining the oil 

Get in there and find your noise, post your findings, I'd like to know what it was

Wild

Wild,

That gravel-road sound is exactly what it sounds like!  I have only been in 2WD so I think I'll have to order a set from one of the suppliers and change those rear wheel bearings as my next step.  It does have 155,000+ miles on it so they probably need to be done anyway.

How tough is the diff gear/carrier bearing to change/rebuild?  Would I be better off trying to find a used diff and get it ready to do a quick swap? This is my DD and my free time is short, so if the rear wheel bearing swap does not change anything, I'll look at that next. 

The carrier bearings are not hard to do, but must have the back lash set
to .008" so if you don't have a magnetic base dial indicator you might
want to have a machine shop press off and on the old bearing races, the
bearings them selves are not attached, but are held in place by a threaded
adjuster rings which by moving sets the back lash and the bearing preload

Dump the diff oil first look at that for problems, and if it's not looking like
metalic paint I would not be worried, just do the wheel bearings, and those
will need to be taken in to have pressed off, it would be easier to get donor
axle shafts and swap them.

I have not heard of too many, or any rear bearings going bad, I'm sure they
do, but not often, I wonder if your diff oil level is OK or low, and did this
happen from lack of lubrication, check that diff oil, pull the fill plug, stick your
finger in to the second knuckle and feel for oil, it should be close to the hole
if not use more of your finger and if none, we have a problem, drain and measure
how much was in there, don't remember exactly but should be around 1 quart

Wild

Thanks Wild.  I'll check the fluid first and let you know what I find!

As promised, I have checked the fluid and it was a bit low - around 6-8 oz and when I checked the level it was a little grey looking but no flakes that I could see.  I got it up in the air and got everything spinning and found that the is a lot of noise coming from the rear wheels; it sounds like the noise I was hearing.  I also used my new mechanics stethescope to listen to all the areas from the tranny back and I found that the tranny was a little noisy but it only sounded like all the gears turning; the transfercase was realtively quiet - I could hear stuff turning; the differential was quiet - all smooth sounds; then, when I put the stethescope on the area where the rear wheel bearing are, it sounded like it was full of sand on both sides!  So that is where I will start and I will update when I get the job done in a few weeks.

Don't want to hijack, but my X90 burned a front wheel bearing the same day as your first post in this thread.
It was growling like a box of rocks and finally gave way. Destroyed the freehub as well as the bearings, but surprisingly not much permanent damage

Good luck in your swap, I'm waiting for parts.

6 to 8 Oz low, or that was what was still in the diff?

The gray would be water contamination in the oil, make sure
the diff vent hose is attached and located high to keep water
at stream crossings out, also you might need to check your
front diff seal, if oil is leaking out it could be where the lost lube went

Wild

Wild,

it was 6-8 oz low,  there was still quite a bit in the diff.  I will check on the other thinkgs you mentioned.  THanks again!

Sprocket,

Hope your swap goes well too.

Just an update: (although a little late)

I crawled under the sammy while it was on jackstands with my new trusty mechanics stethescope and the rear bearings sounded like I had rocks for bearings.  I pulled the axles and overh half the bearing balls were gone on the driver's side and a few were gone on the passenger side.  I got some bearings from lowrange and had a local shop pres them on and now she is as quiet as a lexus with a soft top.

Thanks for all the help.

The wheel bearing replace worked like a charm once I got all the right parts.
Now I'm waiting for a Calmini 3" suspension lift to fit up some 31x10.5s for some fun!!!