It's a nice project, shame it's Intel Atom instead of AMD Fusion though. Looks well put together. Have you thought about spray painting the DVD drive tray to match the case colour? I like using the DIN ports for the fan.
Personally I think the C64X should have used a slot-load DVD drive, it would have looked neater. Using an off-the-shelf memory card 3.5" adaptor is great for a home-project like yours (and it looks very neat on the back), but the C64X could have put these bays over/below the DVD drive too.
Where will you fit the KeyRah, doesn't the motherboard interfere?
