Mind snapping a picture a little further out so we can see more of the wiring?

For what it's worth, here's a couple of Snipit's of the left flipper out of the manual.
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Looks like the gry-yel is in the right spot, same w/the blu-gry.

Can we get a picture of the EOS? Maybe a short across something in the EOS? As Black_Knight mentioned, it sure does sound like the EOS (or something associated with it) is the likely the culprit.

Can you check to make sure the lead isn't shorting out against the bracket? Might as well check the other connection too. Doesn't take much, just a sliver of solder to mess you up.
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Should there be an insulator here? Can't be sure from the picture. You could check the other flipper that is working correctly. Or if it is there, is it worn through?

If I'm not mistaken, the flange needs to be isolated from the leaf switch, otherwise it grounds the leaf switch.

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Yep, that's what I was thinking. Thanks for confirming. It doesn't appear this style of leaf switch has an insulator on the leaf, so the insulator must be on the flipper mech (i.e. heat shrink or the like).

The OP should just be able ohm meter out what likely is a short somewhere. Both during EOS open a closed.

Got an ohm meter?

First thing I would do is to unsolder the EOS from the coil, then check both leads for a short the the flipper bracket. Then manually move the flipper mech to the point it opens the EOS. While the EOS is open, then repeat the test for a short to the flipper between each lead.

With the EOS unsoldered from the coil, the EOS should be completely isolated from the flipper bracket with the heat shrink on the flipper mech.

The one thing I'm not sure about is if the flipper bracket is grounded or not. I no longer have a 90's game to check. So it more about just isolating the obvious, one step at a time.

Yes, the flipper assembly. And I completely agree it shouldn't be an issue. But I don't know the OP's ability (or anyone else that worked on it) - was just trying to isolate things one very simple step at a time for the OP.

Appreciate the comment since it shouldn't be grounded. But for some reason something apparently is going on (i.e. pinched wire under the bracket, etc.?). So sort of asking things that shouldn't be an issue just in case.

I was wondering the outcome too...