The part with the larger diameter threads should be fully screwed into the aluminum "link" component. It is basically a "threaded insert", and once screwed all the way in should not be disturbed.
The slotted screw is where you do your carb synchronization, so the position will vary slightly depending on the sync procedure. One the larger piece is repositioned properly into the aluminum link, I would say that a good "starting" point for the slotted screw is to have four or five full threads showing above the nut.
Kevin in
tx