Hi John -  to AP and the more info you post, the easier it will be to isolate the problem.

I've seen a similar issue on a WMS "Space Mission". The coin switch on the door was not gapped correctly and made contact during the game. Check that the two or three coin switches are not stuck "on".

Sounds like the problem is either the Ball Count unit or an relay activated by the shooting lane switch. The outhole switch KNOWS it is the end of the current ball because it sounds like the bonus unit is counting the bonus decrement.

So whatever is SUPPOSED to be triggered by the shooting lane switch is not. Need the schematics to work that out. I think you are very close to the culprit as this is the stage you are at.

Look at the schematic, and see what coil/relay "should be triggered" when the shooting lane switch is closed.