Ok-- so maybe we can help each other out... I too have a Midway Little League (a quite rare machine!).
Mine has never scored quite right. I've seen photos of a number of these machines now, and it would appear that most of them have some sorts of scoring issues. Please take a picture of all of the relays on the back of the door-- that's where the issue lies.
Most of the problems seem to be not with the "regular" scoring, but with the magic score- is that your issue as well? Could you please describe exactly what's going on and I will compare it to my machine for you.
Your backglass is in incredible condition. Any chance you'd be willing to scan it in so I could have a translite made for mine? My backglass isn't nearly as nice.