- It seems (almost) noone wants / needs external drive bays any more. Waste of space.
- SFX/SFX-L PSUs are getting to the point where ATX PSUs are also a waste of space. Lian Li has a 750W Platinum SFX-L.
- nVidia 980 Ti and GTX 1080 reference cards are 10.5" / 266.7mm . Lower end cards are even shorter.
- Curiously enough, if you add 266.7 mm from the video card and 63.5 mm from the SFX PSU you get 330.2mm which is the SSI EEB size lengthwise.
I would put the fixed 125mm of the SFX/SFX-L PSU to be the height of the chassis oriented so that the cabling runs along the front panel, the power input / air intake side is on the side panel and the fan is on the front panel as well. If you indeed use an EEB board the PSU would sort of hover over the "unused" corner of it, where typically various cable connections are. The vertical clearance should be the close to the same as the I/O panel in the back. If SATA cables are a tight fit within the ~40mm clearance, there are bendy SATA cables available. Since I added an 1" to the side, this arrangement would mean the PSU allows only 10.5" cards in the first four slots but allows one full length 12" card in the three slots closest to the CPU. Even if you have one of those boards where only slot #6 is a PCIe x16 and slot #7 either doesn't exist (Z10PE-D16 WS) or PCIe x1 (Asus Z170-PREMIUM) you still can have a dual slot 12" card in the #6 x16 slot.
Once again, almost like numerology: the SFX PSU dictates 125mm vertically which in the opposite corner means above the I/O panel a 120mm fan fits. Also, once again because of the case height is enough, one 120mm fan in the front should fit as well -- on the Z10PE-D16 WS it would need to clear the RAM modules but that can't be a problem -- DDR4 modules are 31.25mm, shorter than the I/O panel, our defining height. Very nice direct push-pull airflow right across the CPU cooler(s).
On the other side panel, furthest from the CPU, we have space for 2x120mm fans. If you sacrifice slot #1 from the motherboard then you can have a 240mm radiator instead.
Here's how things look height wise: if the case bottom is 0, the bottom of the I/O cutout is 7.2mm, the board bottom is 9.5mm, the board top is 11.1mm, the start of PCIe cutouts is 17.6mm, the top of the I/O cutut is 51.9mm, the top of the PCI cutout is 111.3mm -- numbers from http://www.protocase.com/pdf/How_to_design_enclosures_for_motherboard_based_systems_092010.pdf I hope I read it right.
The CPU cooler height is, after more research is 159mm -- people report being able to install a Cooler Master Hyper 212 Plus in a 4U chassis (see below why it's 4U). In general, tell me why I am crazy
Regarding disks, I am sure we can find some space on the side / front panels. Obviously there is a balance between air flow and disks in a case this small: the internals are barely above 20L which is quite crazy for an EEB case....
Some ideas for more fans as an option: a 180mm fan above the CPU area. It takes away a bit from the height but a Noctua C-14S with bottom fan is only 115mm high (PH-TC14CS 112mm) so a 38mm fan on top would be no problem and an AP-181 pushes a hell lot of air... this would probably make the back fan unnecessary.
Still fans, on the video card side, you need a "protrusion" for the "lip" of the PCI cards. If you take a look at the Sugo SG-02 you will understand what I mean. Now if this continue to the top of the case and is at least 13.5mm "out" then two 140mm fans would fit above most video cards (except perhaps the highest STRIX cards). Since from board edge to I/O cutout there's 148.4mm and from chassis edge to board edge there's 25.4mm, even two Thermalright TY-140 would fit.
Edit: so apparently the case is 4U high. I didn't design it to be so but that's what I/O panel + 120mm apparently means. Most 4U cases do not have 120mm fans in the back but there's http://www.supermicro.com/products/chassis/4U/742/SC742T-650.cfm which does. In the other two dimensions, slice off the ATX PSU from http://www.logic-case.com/products/rackmount-chassis/4u/4u-short-depth-chassis-aluminium-lockable-door-4-x-35-+-1-x-525-sc-43902/ this case and you get pretty darn close to the size of mine. Put together the PCI half of the Logic Case with the I/O half of Supermicro to arrive to the ideal back wall.