"The score motor continually runs, the 4th coil on the right marked "coin" will click twice then advance the coin unit."
If the circuit detects coin drops. The score motor will run. I'm wondering if something got crossed, switch making connection in area where you were working or a solder dropped somewhere. It sounds like the coin circuit is making the game "think" user is adding credits.
I would also suggest reversing the "set everything to conservative in the back box" so you can get back to where you started. Changing everything around just adds more to the puzzle. All that was working fine prior to the repairs you had done.
I also don't think a faulty diode would cause a cycle in the system. They are designed to allow current flow in one direction. Putting them on a coil is more so to prevent DC electronic damage to rectifier from prolonged use. More or less just stopping the current from "firing" back into the rectifier "DC" side when coil activates.