I would like to THANK YOU VERY MUCH Dashingncool because you made it possible for me to have a brand new powerful Mac without having to wait forever for Apple to get to their senses again and to propose a semi-pro computer like I need.
My config is almost the same as yours, except for the graphics card (I took a 970 GTX) and the Ram which is 3200 Mhz 16 x 2
I also have an LG 4K screen, but it's irrelevant here.
Everything is working fine for now, I didn't try Thunderbolt 3 for the moment (I have nothing to plug to it !)
My two cents for the setup
I installed the official Sierra 12.1 release with Tonymac latest Clover (date 11/11/2016)
On the mother board I had to disable the second Lan AND the thunderbolt, the rest is the same as your explanations.
Now I have a big quiet Corsair Carbide 600Q chassis with 1 Tb SSD (2.5"), 4 3.5" internal Hard drives (3+3+4+4 Tb).
Airdrop is working perfectly with my iPad Air 2, I use a mac keyboard (the wired one with num pad), a Bluetooth touch pad from apple and a Steelserie Mouse. All the USB (2,0 3,0 and 3,1 ports) work fine. I have an intuos pad, an usb midi keyboard, a MOTU external sound card and a Fiio external DAC, they work perfectly with all the internal in/out from my sound card.
And I use 2 screens from my 970 GTX : 4K and Full HD
The computer is silent, blasing fast, has a lot of upgradeability possibilities !
With your step by step installation guide, it took me one day to get the computer fully working and another day to copy all the data I had on external drives on my 2012 MacMini to the internal drives.
PS : I let it as 14,2 so it says 2013 iMac but that's fine for me, I don't care for names ;-)
Thanks again ! I ow you