First go into switch edge test to see if all of the associated switches register. Make sure you can hear the microswitch click when doing this. You might just need to make adjustments to the wire actuators.
Usually when the game serves two balls, there is a switch issue in the trough or in the shooter lane. The troughs are optos, so you'll have to empty the trough, then drop one ball at a time into the outhole and see if all of the switches register as the ball rolls past all of the optos.