On the bonus issue first make sure that it is resetting all the way to zero position. There is a switch on the score motor 3A and another on the outhole relay that pulses the step up on the bonus unit for that first 1000. Check that either of those aren't opening enough.

So the question is: Does the score motor do 3 cycles (1 1/2 rotations) before the ball is ready to plunge?

So when the bonus unit hits the zero position the bonus relay should drop out. If it doesn't then a switch on the bonus unit needs to be adjusted. Then the outhole relay is energized. At this point the bonus unit should step once and the shooter coil should fire in the same half rotation of the score motor. Does the ball shooter pulse 3 times as well?

Looking at the schematic the bonus step up should pulse right before the shooter coil. Bonus step up is on 3A and Shooter coil is 4C. Cam 4 is 1 position after cam 3 in the timing.pasted_image (resized).png