Check the J3 connector for issues. Make sure the pins aren't faulty. If they haven't been repinned, it may be time to do so. Also be sure to clean the edge connectors with a pink rubber eraser to remove any tarnish that may have accumulated.
http://pinwiki.com/wiki/index.php?title=Gottlieb_System_1#Display_Data_Problems
If that doesn't seem to result in any changes, take a closer look at pins in question are J3-9 and J3-11. Those operate the D1 and D9 digits on the score displays.
Test for continuity between the connector and the MPU. Then on the other end, between the displays and their connectors. And finally all together from the display boards to the MPU.
If everyting tests good, then it would be time to start looking at some of the chips on the MPU.