When the choke is not active, the jet rises until it's head rests against the bottom of the adjusting nut. So the farther the nut is screwed onto the lower bearing, the higher the jet rises, which in turn allows the needle to fill more of the jet opening and thus leaning out the mixture. The bearing is not supposed to move at all (once it is locked in place by the locknut).
Sorry, I can't really help with the other questions. In my case, a substantial portion of the wear appeared to be in the carb body, so I installed the bushings. The limit, IMO, is when the throttle disc drags against the bore instead of closing cleanly (which was the main thing that prompted me to replace the shafts & bushings).
Certainly it would be possible for the bore to become worn after long operation with the throttle dragging, but I've never heard of it being a problem. And the issue of course would be that the throttle can't close off enough air to bring the idle down. Are you checking this with a new shaft & throttle plate ? Is the throttle plate turned the right way over? (There should be a very slight taper on the edge, that should match the direction the shaft turns.)