Not sure on the game specific stuff, but a couple of general thoughts:
-If you're getting random points with the flippers, is it just the vibration causing a switch to close? Is it one side vs another that seems worse? Start a game with the glass off, and try to shake the machine a bit, or press on the PF-does something trigger?
-You could also just fire up the game in test, go to the switch tests, and see if hitting the flippers closes anything else that you're not supposed to. The switch edge test should show you all of the closed switches, and when you press the flipper you should just see the flipper button and EOS switch (I think). If there's a target going at that point, then there's your culprit.
-The bookcase opto error is probably just a position switch on the bookcase mech. If there's a specific test for it, see if the switch registers in test. Could be a bad opto, or could be something like a wire broken off or loose connector.
Have you got a manual for the game? If not, check IPDB for one-having the schematics for those mechs is handy for figuring out where the switches are, and how things go together/come apart if it comes to that.
Good luck!