You probably have a switch that's not making contact somewhere in the score reels. There's a video on it that Clay Harrell had on YouTube that I'd have you reference, but it seems he's pulled all his videos because of a recent piracy issue. Check out his pin repair site...section 3f discusses score motors, but again, I think your problem may also lie in a maladjusted score reel switch, so reference that section. Sniffing around this site for a while will take a lot of the mystery out of it for you:

http://www.pinrepair.com/em/index3.htm#start

Since you don't know and have never worked on a EM pinball machine before, I suggest you reach out to someone in Madison with some experience. Look at the pin map on this site. start clicking on the dots around you and look for collectors with multiple EM's in their collection. Chances are they're pretty damn good at fixing them.
Good luck.

try contacting this guy presqueisle

OR, you could just sell that junky machine to me.....
Er, how's the playfield??