Your Bonus Unit is not going to the full reset position. Or, at least the circuitry is not detecting this. So many possibilities.

Standard electrical and electro-mechanical troubleshooting techniques apply.

I thought that my BONUS UNIT steps up and steps down, It doesn't reset all at once. Is that correct?
That is correct.

When you say "the full reset position", should it be stepping down several times to get there or all at once?
Yes, it should be stepping down via several individual steps of the (usually smaller) reset solenoid.

I do see the switches changing state when it gets to the reset position (when the plastic post moves the switches)
With power off, press the solenoid plunger of the reset bonus solenoid to get the unit to the "Reset" position. Can you physically move the wiper assembly any "farther" in the "reset" direction? If so, you likely have a physical bind or gummed up parts in the bonus unit.
The rivets and fingers should be mated perfectly and not "off center". The bakelite rivet plate is adjustable. But, as you said, the reset limit switch(es) must be properly adjusted and working. After verifying this, which is one of the most wear-prone moving parts on this machine (after all of the score reels on the game) it is time to get the schematic diagram and follow it to find your problem.