Two days ago, we finally got all components working (sort of) on the stage 2! We sat down and made the serial communication work, there were just some minor tweaks to the code my son had written for the serial controller, and the tiny detail of actually start the serial tranciever after initializing (DOH!) and it worked perfect! 

The parallel port (joystick ports) needed a missing pullup resistor to not have the inputs floating. Small miss but the stage 3 drawings are already updated. So after this, the computer deserverd a beauty shot:

So now the only thing that is left on stage 2 is the IRQ Handler, the 7 unpopulated circuits on the bord (apart from the extra RAM socket).

Thank you PCBWay for helping me making this dream come true!