There are no optos fir the subway, just switches, and it may be as simple as adjusting the switch arm.
As for the balls, not sure what you mean by an even number vs an odd number. There should be 6 balls in there. If it is kicking out 2 balls still then you probably have a bad opto on the trough board. If you take all the balls out you can use a card or piece of paper to to each switch in test mode. You can also use a camera to see if the optos are emitting any light.