For what its worth ive never had to remove a ball trough to install a cliffy eject protector. Ive done it on 4 sterns now and you can do it all from the top side under the apron. Couple wood screws hold down the top of the trough and then it pivots up and out of the way on the bolt on the top of the trough on the drain hole side. You may have to loosen that bolt/nut.
I know that is usless info now, and im not the guy to help debug switch matrix stuff. So sorry about that.
Im reading along hoping to learn. Good luck. Im sure pinside can get your game back soon.