Some critical note's from a self PC builder here (sorry).
I made allot of PC builds and see some obvious problem here, "no place for massive GPU's". There are nice cheap bare bone cases available that have support for a large GPU card.
I ones made such a system for a friend and it was very small jet very powerful for gaming and all sort of high demanding software. It housed a mini ITX with Sata600 support driving two SSD's in raid 0 a core i5 CPU and a GTX660 GPU. (all in a very small package jet there were no performance tradeoffs here)
There are smaller form factor PC's with lower spec. graphics already available, so I don't see the reason for your form factor here.
It's a nice design though.
Al in all I think this is a nice case study for 3D printing product design and good learning experience.