I have some of the issues you describe on my Big Indian, but not to the extreme as yours. Each letter lane has two switches - one for the light and one for the score. I still have to refer to the schematic to narrow it down (just haven't yet), but on my BI, I find that if I only trip the light switch for a letter lane (e.g., bounce off a pop bumper partially into a lane), the special can be lit, but it won't score unless both switches of each letter lane are tripped. Its possible that there might be some lane switch adjustment/repair needed for the lanes on your machine - but if all are exhibiting the same behavior I'd suspect something further along in the circuits.

The credit scores are set by plugs in in the back box (even player side). There should be a placard on the inside of the backbox that shows the proper plug placement for the various scores. Likewise the various plugs in the cabinet should have an associated placard describing the settings - one of which is the number of balls (which affects rules some). Let me know if you don't have the paper placards and I can get you pics.