IDC connectors often fail where the wire is pushed into the connector. This could be the case on your game if the old board and the new one are doing the same thing. Re-seating the connectors to the board wouldn't change much. Now if it is a connector with this issue, I wouldn't know which one. Sometimes you can get a problem like that to surface with gentle wire wiggling while the game is on. If one has an effect, re-pin it. I hope you didn't toss the original MPU. It is probably still good.

Swap the PS with one of your route games just to test it.