If all else fails, I have found that just a single strand of steel wool caused crossover problems.
I once had a problem where a strand was on the front side of a wiper board, and never noticed..
If nothing else solves the issue, it wouldn't surprise me if there's some sort of crossover on the
backside of the BCU's wiper board..

By disconnecting the Y-R wire, you cut the circuit to the common yellow, so although there's a crossover,
the 2nd Player Up lite would not lite. After starting up a game, can you pick up each bcu's wiper blade to find which
blade(s) control the up lights? Once you figure (maybe you already have) which rivets on the wiper board control
the Up Lights, you can strike a razor blade (knife) between the rivets to make certain there's separation between
those rivets. I've done this more than once to fix crossover problems. I remember last winter, even on the wiper
itself of a ball bowler, I took a razor blade knife and sliced between the wiper insulators on the hub to fix a strange
problem. If I hadn't noticed a small ache on the score motor's wiper blade hub, I would have been scratching my
head for quit a while..
I have also had crossover problems on the backside of wiper boards from very tiny metalic objects..
I actually have an Aladdin's Castle in a local Pizza Shop. It's about that time to freshen it up anyways, so tonight
I'll stop over there and see if any other ideas pop up, but my guess would strongly be rivets crossing over on either
the front or backside of the bcu's wiper board.. (Possibly the wiper itself, but not as likely)..

Okay, and a continuity test on a "1st Up" rivet, and "2nd Up" rivet should say if a crossover
sits there. This can be done while in the Off position, keeping the pacemaker on pace..

I'm so glad that you found the problem. The ones that exist that do not exist on the schematics
can be the most tricky ones..
I've found so many throughout the years, that I'm kinda getting good at them..