After spending about one hour, per hub, picking out little metal shavings, I reassembled everything one last time.
And what do you know, everything turns nice and free like it is supposed to.
Concerns/Observations/Theories/Etc.
Does the wheel hub assembly need a thrust washer? I am really not sure. If you stop and think about it, the wheel bearing thrust washers are usually tabbed, to key into the notch in the spindle, to prevent them from spinning. Is there really a difference If the bearing inner cone is against an immovable washer or the nut it self, I don't think so.
When I removed the thrust washers, I was concerned that the inner nut would bottom out before eliminating all the bearing play. This fear was unfounded. Even without the thrust washer, the inner nut, when tightened down, will "seize" the bearings. There is no extra apace between the end of the spindle threads and the face of the outer wheel bearing that needs to be taken up by a washer.
This rear wheel bearing hub, while similar to a front wheel hub, has one important difference: bearing end play. With a front wheel hub, you usually allow a "hair" of in/out movement. On these rear wheel hubs, there is not supposed to be any lateral movement. On the inner nut, you tighten it until it "seizes" the bearings, then back off of it just enough to get the bearing spinning free with no in/out play. This is per Warn's instructions, and in all my years/miles of driving this set up, I have never burned up the bearings.
Since there is no lateral bearing movement, is a "thrust" washer necessary to take up the bearing to nut movement/interface/friction? I don't think so.
The instructions I am using came with the New Warn Full Float axle kit I installed in the back of my red Scrambler. That kit used thrust washers, everything assembled fine, and everything works fine. Due to the fact that these kits were made for several years, and probably had design changes throughout this time, different kits may have differences. I would have to pull the red Scrambler and the tan Scrambler apart to verify, but I believe that there is a difference in these two kits which allow thrust washers to be used on my red Scrambler, and not used on the tan Scrambler. Either a spindle nut stack design change, spindle change, something.
Also note, the tan Scrambler outer spindle nut came pre-drilled with threaded holes for set screws. My red Scrambler kit spindle nuts do not have this feature. Maybe the tan Scrambler kit is an "earlier" version, and I do not have the correct instructions for this "early" kit.
And if you are still concerned about thrust washers, here is a picture of Warn's Front hub conversion:
It is a little bit blurry, but you can clearly see that NO thrust washer is used between the inner spindle nut and the outer wheel bearing. I have installed this same front hub kit on my old CJ-7 and my red Scrambler, without "thrust washers", and have had ZERO issues.
So, is a thrust washer necessary on the rear? I am not an automotive engineer, or even a mechanic, so I can't "say" with certainty.
For me, I am going to run this rear axle without thrust washers. I will closely monitor the rear hubs for any problems/metal shaving/play or any other problems. I don't anticipate any issues.
"IF" I have problems, there is only one way that I know of to add thrust washers: I will have to machine down the back side of the inner spindle nut to the same thickness of the added thrust washers, to effectively keep the spindle nut "stack" height the same. This should work.
Like I said, I don't "think" I will have problems, but if I do or don't, I will update.
That's it for now.
But, if I was running a Dana 44/60, I would definitely install them
I ended up replacing the hubs with the drive flange kit and haven't had any problem since, well, unless you call a little gear oil seeping out a problem. Ironically, it's on the side that I replaced the spindle seal and outer bearing on when I repacked the bearings after the hub incident. The locking hubs would be just the ticket for flat towing--which I don't do, but I didn't trust them enough after that to look for another set. I know they are difficult to find now. 
