I would start at the power supply. You have a new p/s, so I would make sure all the connectors are solid and that you are getting proper voltages to the other parts of the game.

All the connectors you found have a mate somewhere in the game. Look closer, they are there somewhere.

If you are using original boards, you will need to replace the 40 pin interconnect board between the mpu and driver board.

I would also replace our at least check that your sockets are solid. Either the interconnect or sockets could be causing your intermittent boot up issues.