Looking near that jones plug:

If I had to make a wild guess, I would wonder if the 0-9 (ones) unit is designed to score 10,000 points when advanced?

If so, I would check the wiper positions on the unit (unlikely) then the rollover buttons on the playfield (more likely) that advance the 1-10 to see if one is stuck down or possible shorted.

The other way to state this is: when jones is unplugged, what on the playfield DOESN’T work? Isolate your search to only those switches, because one is stuck on when you plug the jones back in.

No. But if the problem disappears when this plug is out, it stands to reason the problem exists only when the plug is in. So, if when you unplug it, you disable two switches and a rollover, it stands to reason that when you plug it in, you enable those three, and one of them could be the cause of the issue.

This is just a theory. At least now your search is narrow and you can see if I am right or wrong in a matter of minutes.

I am wondering if when you replaced the pop bumpers, you accidentally smashed one of these other switches with your elbow. I would plug it all back in and physically move these switches from underneath and the wires near them to see if I could get a reaction. Check the switch blades, the solder points, and any stray wireforms or missing insulation.