You're in very good hands with Mopar-- he's more knowledgeable about this stuff than I am.
With regards to game selection, I assume you saw this old thread of mine, and that's why you PM'ed me (https://pinside.com/pinball/forum/topic/a-couple-of-shuffle-alley-questions). In the end, I never did remove that jumper (though I did solder it in rather than using alligator clips). I never could figure out why it wouldn't "lock into" a particular game, and the fix, while a little hacky, did work.
>the lock relay does not energize so this makes the game over coil drop out and the plate goes all the way to the rest bar, see picture.
I can dig out my schematic later, but if you happen to have a close up of this part of the schematic we may be able to work through this quickly. I'm not quite sure I understand from your description what is going on-- is one of the latches becoming unlatched when it shouldn't? Or is it not latching when it should?