I just was working on a Gottlieb Em exhibiting sort of similar behavior. One of the score motor switch stacks had shifted just slightly so that the leaves were not sliding through the slot so they could close when the indentation in the cam came around. The stack never moved as the score motor turned, so the switches never close. For awhile it was intermittent; it would slide partway through and trip sometime and sometimes it would trip temporarily. Dunno if you're having that issue, but since the score motor sounds like the only thing you haven't looked at... ?

This. Let's see a pic of the pins of that jones plug as well as the solder connections. Sometimes pulling a jones plug a fraction out from the bottom helps make contact on a clean part of the plug and can show you where the issue is. This shtuff like this can usually only be truly solved by someone live and in person.