Quoted from pindude80:
Thanks for taking the time to type this description out. I will give it a try. I do have a question though, will a stuck switch show up even if it's not putting a 2nd ball in the shooter lane? Getting the 2nd ball is random and happens at ball save when I'm in the middle of a game.
When something unexplained happens during game play, since you are at home, open coin door and enter switch menu, forget about your game a minute. Suppose you have 5 balls in the trough, one in the shooter lane and one stuck under a sling. The game should show: 5 in the trough, 1 in the shooter lane, 1 pressing on sling switch and 1 open coin door switch for a total of 8. What I am trying to say is that the switch matrix shows what's open or closed at any moment.
Note-with 2 ball issue, you would expect to see 5 balls in trough, 1 ball in shooter lane, the other ball in shooter lane won't register, and 1 open coin door. Maybe that won't solve your 2 ball issue since that is a known bug, but it should rule the switches out as the cause. Using the switch matrix may help track down other issues later.