First Problem: Here's the diagram of the finger position of the Bonus unit on a Space Mission (4 player version).

2nd Problem: If you are talking about the switch stack in that same bonus unit. The spacer must have fallen off of either the top or the bottom. Try it both ways and see which way opens and closes the switch correctly.

3rd Problem; When adjusting switches you don't actually bend them. I've seen many poorly adjusted switches with bends in them. I would say that you "lean" them in the direction you want them to go. i place the contact adjuster near the back of the stack and softly twist the tool the way i want the switch to go. I use a gentle rocking motion. Sometimes I'll move along the length of the switch putting tension on different areas of the blade. I do this so lightly that I may have to do it 5 or more times to get it to move to the proper position. When you are done adjusting the blade, there should be no obvious bend.
bu1 (resized).png

It sounds like your machine is in a Game Over state. Check the switches and the interlock function on the game over relay. One coil should lock the switches in one direction and the other coil should unlock them to the opposite state.