Guess this sounds silly but did u check the connector for 12 volt on the driver board. Its on the left hand corner of the board right under the fuses. that said im thinking now that if the game picks up the balls and that means there should be power to the optos in the game.
If a row or collumn of switches is out the logical thing would be a broken wire or a cpu board issue.
Find the opto in question and test for power. If u dont get power u should look for a broken wire. if u do get 12 volt, my next step would be to test opto itself by going into test mode in the game and then shorting the two wire together for the Receiver. Read again only for the receiver, u dont want to short the transmitter 12 volt. The opto with the black housing is the receiver. In switch test u should see it register when u short the wires together, if u dont u probably have a broken wire.