The first part is easy; the game is seeing balls in the trough and is trying to remove them; that is why the it keeps kicking a ball to the launcher; when in game the same is sort of true except the game also sees that there is a ball blocking switch 67 (trough up) this tells the software that the ball never made it into play, plus the program sees all your balls are in the trough...
So why is the ball trough photo transistor board not working and causing a ground short on Row 7 when 6 balls are in the trough?
This is a very odd indeed...but, all these problems point to a failure of your ball trough photo transistor board. A shorted D5 on this board would cause a ground short on Row 7 whenever it was pulled low, but this should only be when the opto is clear which would also be a closed switch 67. Normally opto switch 67 would be closed all the time, but yours isn't; your S67 doesn't close until you install a sixth ball in the trough, this makes no sense as the sixth trough ball is switch 61 and is on a different LM339 from switch 67.
In order to really see whats going on you are going to need an o'scope...maybe you have one?
I'm going to speculate that when your drop target switch wire broke, it came in contact with the solenoid voltage for a moment, this voltage would be sufficient to damage your LM339's on the trough board...the only thing I don't like is that this happening will usually take out U20 on you MPU.
I've included a couple images that show the normal operation of the LM339 on the opto board.
Unblocked Opto - Row is driven LOW while its column is active, this is why unblocked optos show as a closed switch.
Opto Clear (resized).png
Blocked OPTO - Row is driven HIGH while its column is active.
Opto Blocked (resized).png
If you would like to send me your trough board, I would be more than happy to take a look at it for you...Just PM me.