OK - I had a similar issue with a Fathom years ago. The F5 fuse was getting hot and eventually blew because the ground strap on the lower section of the headbox was touching the GI on the light panel of the headbox. It happened every time I closed the light panel. So I think you have a short to ground on the GI.
I'd like to try removing F5 and checking if the game works 100% without GI. At least it is narrowed down by the sounds of things - GI short to ground. The other thing to try is checking continuity between the F5 fuse clip (just do both sides) and the ground braid of the machine - with the game off.
