Have you replaced the connectors? That's the first thing that comes to my mind when you say it's happening across multiple columns, that maybe you have a short across / inside one of the board connectors. I wouldn't worry about repinning at the board side, since you seem to have a new board rather than an OEM, but I would def get some molex connectors from GPE and replace everything going to your MPU, and probably the large connector that collects all the wiring beneath the playfield and runs it up to the MPU.

Also, you've put this in my head.