Could you post a whole pic of each board, old one and new one? Based on the CN nomenclature for the connectors of the new board, i think you may have a Data East power supply board there. (Though I may be wrong about that, perhaps it's an aftermarket board?) If it is a data east board, I don't think they can be used with your game, but i don't know enough to be 100% sure about that.
Either way i wouldn't recommend turning the game on until you are certain the board is compatible with your game and figure out the wiring issue. Something definitely doesn't seem to be adding up...