Update: Added rear panel used Michael's rear panel as the cut out, added DVI and two additional DB9s as optional pop-outs at the rear, still sticking with the cartridge at the top aligned directly with the socket at this stage, tweaked the design slightly to accommodate the cartridge slot.
For those that were following my case just an update that I 3d Printed a draft of the back panel to ensure the ports aligned and that the pop out panels worked.... and it did, perfectly!
The USB connector was 100% that was the big test, the pop outs worked as designed, and I placed my RGB connector from the Sophia in one of the spare DB9 pop-outs, holes aligned too! Im adding three DB9s now in case someone wants 4 joystick ports and the Sophia running.
Just waiting on some new printer parts to trial a print of the whole case.