God I'm so awed by your project and love it so much guys! But where's the beef? What kind of can are you going to pack it in?
I don't do electronics or PCBs (at least not in the past 25 years, but what I do do is look a form factors, available cubic and stuff things in where you'd least expect. I've been looking at the Q700 PSU for a very long time, mostly to adapt the stock can to power my Quadra 700/8600/G4 project that uses entirely different connectors. I tore up one Q700 PSU for nefarious purposes, so I'm passing familiar with the hardware.
Please don't take this as criticism, none is intended, just "inside the box" suggestions so to speak. I have trouble visualizing how you'll be using your PCB in the configuration above? How's it gonna work, at least with the stock Apple can? Are you modifying it heavily or not using it at all? The only thing that makes sense to me would be mounting the FlexATX PCB to the lid so it hangs upside down next to the stock IIcx form factor cooling fan with its funky black top/housing. You can mount your board to the floor and leave all the extra wire between PCB and the ATX connector on your board. The wires are overly long, but at least they'll be hanging down in a coil to plug into your card.
However the 10-Pin connector on your PCB . . . I can't see that working at all. Harvest the original 10-Pin plug and wires from the stock supply and hardwire it to your board. Apple's funky connector is engineered to do a lot of things that would stress the connector on your board well past the breaking point.
Besides the thicker traces,
PLEASE provide mounting holes on the board to bolt it down to the floor, lid, side or wherever is most convenient on the inner surfaces of the stock cans? Think about my suggestions, set up that way in the original can with the original 10-Pin harness and it should be ready for plug and play . . . ruggedized per Apple spec.
There's a LOT of mechanical forces going on every which way between the Apple's custom connector(?) hanging from those two metal flanges and the square cone shaped entry of the board socket during installation and removal. :approve:
p.s. bonus points for conserving the A/C input and monitor passthru hardware to perfectly match the openings in the back of the case.