If all the switches were working correctly, it wouldn't keep launching balls. Period.
If you are 100% that there are no problems with the subway diverters, vuk's and their corresponding switches then the problem is in the trough.
The transmitter boards get the crud beat out of them because williams attached it to the coil bracket that loads the ball. Try jiggling and bumping the wires while there are no balls in the trough and see if and of the optos register. Because the components on the board are old and huge, they shake a lot when the ball loads and give a false signal. They would work during test, but not when the game is loading balls.
If you want to salvage the transmitter board, pull it and reflow all the traces for the components and pins. While you are at it make sure all the wires are tight in the molex connector.
Quoted from Push600:
More information. When a ball is shot into the start mission hole, during multi ball, it does not find it.
Is this still happening? If so, then you know what opto isn't working. Fix this first. In case you didn't know, if you look at an opto transmitter with your cell phone camera, you will see it glow if its working. Sometimes the transmitters just get weak.