I would suspect the "missing tooth" is factory. what type of stepper unit is it ? "increment/decrement" like a bonus unit -or- "full reset" like a player-up unit?
Yeah those rivets look pretty worn , myself I would probably try to fill them with solder but apparently they can be replaced https://pinside.com/pinball/forum/topic/gottlieb-stepper-switch-rivet-tool-help-pls