Before spending too much time looking into that EOS switch, I would confirm that the fuse holder is good. Most GI issues I've seen in Bally games have been caused by those crappy fuse blocks.
There are a couple of Jones plugs junctions leading to the Bonus unit as well as at the beginning of the GI.
Try cleaning all of the male jones plugs with fine sandpaper and make sure the tabs on the female plugs are tight. Also make sure none of the wires are touching on the tabs of the plugs.
Bally's female jones plug connectors are generally more problematic than Williams or Gottlieb.
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