Well you covered most of the bases. Rusty hit it on the head as usual. Unless you're 100% certain that the noise is coming from the box itself (and even if you are
), the hub(s) are usually a good suspect to check out.
As is a front driveshaft of course. Even though the clicking is not present in 4-low, the dynamics can be just enough different that a noise might not be the same in low as in high. So while perhaps a longer shot, still worth investigating at this point.
And yes, I think you're correct in that the two rods should be equally out when in 4-high. Same as both all the way in, while in 4-low I believe.
Others will know that better, but pretty sure that's correct.
Paul