To add to what godolddays has said: The Bonus unit should count to zero when the ball hits the out hole. Also went the ball is released into the shooter lane the bonus unit should step up once at that time. If it doesn't power will not be transferred to the out hole switch and so nothing will happen when it is pressed.  Turn the machine off, manually set the bonus to zero, turn the machine on and start a game. See if the bonus unit steps up once when the ball is released. If it does then test for 24 volts at the out hole switch to the black common. If no power there may be a bad contact at the bonus unit. It sounds like you are close to sorting this. keep up the good work! 

P.S I can't see the flipper switches will be related. Maybe its the vibration causing a bad contact to make is my guess.