Oh boi. I'll just say it.
Shame on me - I missed a couple of diodes.
The bumpers and flashers were still "unprotected" and on top of that, the LED's I had installed were double polarity meaning they worked in both directions.... Who could have known, right?
The good news are that lights are now working somewhat properly (we'll get to that) and I've updated the main board with the correct lights and what not. This means I'm kinda back where I was before recreating the light board. And that's a good thing! I've also fixed sound and music, which had a few bugs that has stayed uncorrected since moving to the new system and board. Tried a couple of quick games too. 8-)
The bad news is that there is a slight flickering when a couple of lights are active at the same time. This flickering occurs on the light board itself as well, so it may be due to lack of power in the board or shift registers. I'm currently using a row/col based approach, which lights up to 12 lights per channel. I will try converting to col/row so that each row only ever power a single light at once. Hopefully that solves things.
I've also noticed that the servo handling the target bank was dead.
So I replaced it, only to find out that that servo too died after a few on/off's. The servos are beefy ones and are moving up to 5kgs, which is more than enough for the purpose, but somehow they die anyway. This last one has frozen in place, unable to turn, but it sounds like it's working. I'll have to investigate this further.
On top of that, the captive ball lane captures balls despite having no ball lock. The irony...
Code revision on the game will have to wait until the servo is corrected, as well as the captive lane.
But yeah, progress! \m/