I appreciate that it sounds strange but I believe I have eliminated everything else. With the gears removed and only only the leadscrew thrust bearing, two lock nuts, coupling and clip installed, when rotating the handle the carriage couldn’t be smoother in both directions. With even light finger pressure, just enough to hold the coupling from rotating, the jank begins, and through my finger I can feel the intermittent little scratching and grabbing.
Repeating the same test with the clip removed, the jank is nowhere to be found. I can flick the coupling and watch it spin very freely many rotations. It stops dead when clipped. It could be a burr or something on the inner face of the coupling, or burrs on the leadscrew groove similar to what is likely holding on the coupling, but it’s clip related either way.
Worth noting I think this machine has probably only seen an hour of use if even. No wear anywhere, the original brazed tools the previous first and only owner bought with it are still wax sealed bar one, which shows little use.
If there is a break in period that usually wears these kinds of things in, it hasn’t happened yet.