It could be that the Bonus relay is dropping out one step too early, when the Bonus Unit is at 1000 instead of at 0. There are two switches on the Bonus unit that need to stay closed until the Bonus unit reaches 0:
Space Mission bonus relay (resized).jpg
These switches may be activated by pins on the stepper gear rather than the wipers. Figure out where they are on the stepper and then manually advance and reset the stepper to see if they change only when the stepper steps in or out of 0.
/Mark