I wouldn't consider moving anything until you test the optos in the switch test menu. When we walk up to a new game on the line that's among the first things we do. Enter the menu and drop a ball from the middle playfield. I don't remember what they are all called, but you should see three optos trigger as the ball makes it's way down the subway. I've fixed quite a few issues in that right subway on final testing and it's rarely the opto positioning.
Edit: That said, if your scoop is not registering shots that is the opto you should be checking. Obviously, in game, it will only be registering for things like mode start, extra ball, spacium store, etc. If you are not getting to those things, it's 100% that opto. It should be labeled near your Pinotar (red board). Give us a call on Monday if needed. We'll get it working or send you a new opto pair.