If you lose 12v power to a transmitter opto or it fails to be bright enough for the receiver to see the IR beam, the game will think there is a ball there that is blocking the beam and will fire that coil.
Also, the game doesn't detect enough balls in the trough or where they are supposed to be staged, the game thinks there could be a ball stuck there.
Another possibility, is that you may have had either the J206/J207 or J208/J209 switch matrix connector come loose at the bottom of the MPU board. May want to reseat those as well.
If any of that is no help, I suggest doing a switch edge test on all the switches and optos in case you have a whole row or column happened to fail.
I bet is that a cable connection came loose though. Wouldn't hurt to clean that opto pair in the auto launch lane.