Blimey...no one can come here screaming at you
Looks like you have a pretty darn good idea of what you're doing!
I recommend finding an old mATX case somewhere, and cutting it up to give you the backplane, and the motherboard tray (which can be cut down to just the right size you need). This will help you to keep the PCI cards still, as if they move around, they will cause the computer to jump, or worse, lock up totally.
How are you going to control the system? Touchscreen overlay on the 12" display? Keyboard/mouse, IR/RF remote? My vote goes for touchscreen
I look forward to seeing this project come together, make sure you take lots of piccies!