For the ball drain scenario specifically, the flow should be something like the below:
1. Ball goes in the drain and closes the outhole switch, which causes the bonus relay to energize
SM_01 (resized).jpg
2. Bonus relay switch closing starts the score motor
SM_02 (resized).jpg
3. Bonus relay switch closed with the score motor turning causes one of two things to happen repeatedly until it reaches its zero point:
SM_03 (resized).jpg
a. Bonus unit reset fires up to 5 times per revolution and 1000 pts is scored each time (double bonus inactive)
SM_03a (resized).jpgSM_03a_2 (resized).jpg
b. Bonus unit reset fires up to 2 times per revolution and 1000 pts is scored twice each time (double bonus active)
SM_03b (resized).jpgSM_03b_2 (resized).jpg
4. Bonus unit reaching zero de-energizes the bonus relay, and causes the outhole relay to energize once the score motor finishes its revolution
SM_04 (resized).jpg
5. Outhole relay switch closing starts the score motor
SM_05 (resized).jpg
6. Outhole relay switch closed and score motor cam 1 switch closed fires the ball count unit step up (i.e. advancing to the next ball number)
SM_06 (resized).jpg
7. Ball count unit step up EOS closing causes the player reset relay to energize
SM_07 (resized).jpg
8. Player reset relay switch closed and score motor cam 2 switch closed fires the player unit reset coil (i.e. resetting back to player 1)
SM_08 (resized).jpg
9. Outhole relay switch closed and score motor cam 3 switch closed fires the bonus unit step up coil (resetting it back to 1000 for the next ball)
SM_09 (resized).jpg
10. Outhole relay switch open and score motor cam 3 switch open de-energizes the ball index relay (resetting it until points are scored on the next ball)
SM_12 (resized).jpg
11. Outhole relay switch closed and score motor cam 4 switch closed fires the ball release coil (kicking the ball into the shooter lane)
SM_10 (resized).jpg
To keep it simple for troubleshooting, this assumes a single player game, no extra ball active, some points have been scored (energizing the ball index relay), it's not the last ball, etc. There are also some minor things omitted that fire elsewhere in the schematics or the paths that keep these relays locked on after energizing. But hopefully this gives a general idea of the flow for troubleshooting purposes.
Feel free to ask questions or let me know if something doesn't look right, this is based on skimming the schematics quickly while I'm at work. I do admit too that there are a couple things that don't make sense after typing this up (like how exactly the long dwell cam timings work for the double bonus 1000 pt scoring).