This is my game development workstation built with the latest Skylake chipset and motherboard as of February 2016, intended to be somewhat futureproof and upgradeable.
It is optimized for fast compile times in Unreal or build times in Unity (with IL2CPP) through use of high speed RAM and SSD (you will want your project files on the SSD drive (C:) and not the 72000 RPM one.
Something worth noting is that the motherboard has no wireless network capability. Ethernet only. And there are no extra internal (PCI) slots for a card. So if wifi is important to you, then you'll need to go with an external USB adapter for that.
The Z170 motherboard offers two USB 2.0 and six USB 3.0 slots in the back in addition to the 2 USB 3.0 slots passed to the chassis's front.
The handle on the Mini ITX case might be useful for potential transport to trade shows, although I am not comfortable with that due to the precarious looseness of the T2 CPU cooler. One jiggle on the case might loosen it.
The liquid cooled hybrid graphics card helps support a smaller space for air circulation within the mini-ITX. Assuming you are not a graphics programmer or artist, GTX 970 was used instead of GTX 980Ti to keep cost down if you are on a budget.
0) Place RAM in before securing the T2 CPU cooler. The cooler fan will rest on top of the RAM and you won't be able to slot those DDRs in if the CPU cooler is in place
1) The T2 CPU cooler does not have much clearance within that chassis, and so you will want to make sure it goes on before mounting the motherboard
2) You also want to make sure the T2's fan is blowing in the same direction as the chassis fans, front to back
3) Other coolers are probably fine as long as the dimensions are roughly that of the T2 or smaller
4) Audio HD connectors are under the decorative EVGA IO cover. I recommend connecting the audio connector, then putting that EVGA IO cover in place, then mounting the motherboard
5) The IO Shield is padded. I had to tear off that padding in order to get the mounting holes in the chassis aligned to the motherboard when it is flushed to the back of that miniITX case. I'm kind of a newb at modern rigs, so maybe I'm just ignorant of something obvious here.
Summary: RAM -> CPU Cooler -> Connect Audio wire from chassis to motherboard (listed as item #20 on the motherboard diagram) -> tear off padding on the IO shield before snapping onto back of chassis -> Mount motherboard+CPU with RAM, cooler, and IO cover in place. Note that IO Cover is specifically a different piece than IO shield.
For some reason, I could not get the RAM to clock at 3200. Motherboard boot would fail to post when I did so. CMOS reset button on back of the motherboard is your best friend when experimenting with BIOS. I ended up leaving mine at default after several failed attempts to use the settings/loaded profile from the RAM chips.
There is no room for an optical drive, so you'll want an external DVD drive. Installing windows via USB flash drive failed. Not sure why, but others also had that problem. Installing windows via external DVD drive worked fine.
On the subject of which hard drive to make your primary, there are pros and cons to both.
If you make the SSD drive your C drive, You get the benefit of superfast bootups. Also, Windows 10 has a nice feature that lets you specify the location of many user folders, such as "My Documents" and "Downloads" so you can point those to the terabyte D instead of 250GB C. You'll still need to point Chrome to your D:\Downloads or whatever folder, though.
But... A lot of programs (like Visual Studio 2015 and Microsoft Office 2013) do not give you a choice of installation location, and so they will place the app on your C: drive without asking, which can fill up your C drive faster than you'd want. In retrospect, I should have made my giant terrabye 7200rpm drive the primary C: drive and the SSD the D: drive. It would mean slower booting on Windows, but I'd at least have better control on what gets put on that SSD and also avoid the hassle of having to be vigilant every time I install something.