I'd be looking at the power supply, but that has already been replaced. I would assume it is ok. I'd be looking at the connectors from the machine to the power supply board.
It won't be the transformer. It will be something more simple. It can't be the flipper coils - unless one is faulty and there is an over rated fuse. If a flipper coil was suspect, it would blow the fuse. If the fuse is over rated, it would cause issues further upstream - in the boards.
