DISCLAIMER: before reading this dissertation please have at least two beers or two mixed drinks as it will help to loosen your mind, intellect and comprehensive abilities.
Since I don't have the parts to put everything together I have been cleaning stuff and thinking. What happens when a shaft gets hot? Well, it expands both diametrically and longitudinally. That means when it is cold and you set the end clearance between the shafts and it gets hot there will be less clearance hence wear on the ends of the shafts. The ends of my axles did have signs of galling but not badly. I stoned the ends of the shaft to smooth them out and I am having a conference with myself as to how much clearance to set it at cold.
My mind tells me that the axle housing will also expand in diameter and length as well so the question is how much and are the expansions of axle and axle housing equal? Now, the spec is .001" to .006" so what is safe? The friction of the gears will heat the oil and the oil is slung around the center section with the heat starting there and migrating outward. At the same time the axle shaft picks up heat from the ring gear assembly and that heat migrates outward. One axle is shorter than the other as well as the housing on that side and will heat up faster from conduction more so than the other side which is longer.
Another consideration is, the oil is, for the most part, contacting the bottom of the axle housing more than the top so will the bottom expand more than the top? If so that puts negative castor in the axle housing. Did the factory allow for that when it was cast and machined? Will it make a difference?
In class 8 trucks the front wheel bearings are set loose. You tighten the axle nut by hand until it stops and back it off a very small amount so it is just a little loose. If we apply that concept to the Jeep axle then we are achieving the same result. I have seen more taper bearings fail from being to tight than to loose. When you consider the ends of the axle shafts rub if everything expands to much, then my better judgement says loose is good, tight is bad.
So, again, what is to loose and what is to tight? At this point I have applied the long used "SWAG" engineering term. With SWAG as the indicator I have rendered my opinion that an end clearance of .004" should be adequate to eliminate any issues of galling of the axle shaft ends. In as much as the axle shafts will dance back and forth against each other and the bearing cone, then the .004" should keep everything real happy in the rear axle housing.

It always helps to think a lot while your working.

UPDATE: last night I was cleaning the left side backing plate and found a thick shim stuck to the back of the backing plate. That would put it between the backing plate and the bearing cone retainer. Thinking about that I decided the last owner must have known something about the axle shaft end clearance and put the shim there when he found to much end clearance with the shim in the correct place and didn't want to loose the shim so stuck it there.
I would very much like to disassemble the center section to see how they tick but I sure as hell don't believe in fixing something that isn't broke or I don't think is broke so it's not coming out now. I am considering putting a limited slip center section in the rear end and if I do I'll have time to play with it.
The pictures of the part layouts in both my manuals and the parts manual don't show the detail I desire. Nor do they list the bearing cone retainer plate that holds the cone in place. Some show it but none list the part. There appears to be a sleeve that rides on the shaft that supports two of the bevel gears and can slide back and forth to abut the ends of the axle shafts.
I have to remind myself I am not repairing a pocket watch and it's just a Jeep rear axle.