The player one 100 point reel switches are likely out of adjustment. Try pulling out the 100 point reel from player 2 100's reel and compare the switch positions to the player 1 100 reel as you cycle through the numbers. There are 3 positions for these switches: Position 1 at "0", position 2 "1-8" and position 3 at "9". Below is a link with some good pictures.
https://homepinballrepair.com/em-score-reels-gottlieb/
The bonus on this game is usually difficult to dial in. I've recommend the following:
1. Clean the rivets on the bonus stepper (under the play field) so that they look clean like the ones on your player unit. Also check the alignment on the stepper.
2. When a drop target drops it hits 2 switches. One is a switch the temporarily closes that triggers the immediate 500 points and a 2nd switch that remains closed and is used in circuit with the bonus stepper to score the end of ball bonus. Make sure the switches that remain closed when the drop target is down are clean.
3. If you are still having an issue you may want to check the travel of the plunger at the bonus unit to ensure you are getting 1 clean step each time it moves.
Also, is normal that the bonus unit steps 15 steps when each ball ends. This is the scan of the 15 pool balls for the bonus. Note the bonus stepper has two speeds...fast for pool balls(targets) not down and slow for targets that require scoring.