@kgp: First of all, kudos to you for your great build and post!
Okay, my comments might not be relevant, given that I am still on El Cap, but I have built a system based on Giacomoleopardo's guide and I did have an occasional hard lockup. As I have an almost identical hardware build to his, I was curious about what was the cause.
Thoughts about crashing: one thing I did was upgrade the bios to version 1401. The next thing I did was start using an external usb audio source (probably not the issue, but I was experiencing some audio skipping, which has not happened since I went to usb). I also don't use Thunderbolt or USB 3.1. I've experienced absolutely no issues since then (a couple of weeks, with extensive use of the system - almost every day, 8 hours a day). I also, in the bios, turn off usb ports I don't use. This is my alternative to setting up an usb dsdt and using uia exclude in clover. I have no more enabled ports, usb 3 and usb 2 than the 15 port limit.
Failure to boot an install disk: some times failure to boot an install usb depends often on which usb port you choose to try and boot with. Those who are having trouble should read the guide carefully, and make sure they have followed the instructions (its easy to miss something - it's happened to me), and make sure they use a usb 2.0 port, like the one under the ethernet port. Why? Tonymacx86 can answer that better than I can, but this is something that has caught me more than once - I just forget to remember that this can often affect whether you can boot your install disk or not. One time, despite a decent amount of experience, installing many times, I forgot to create the install usb disk as UEFI bootable. Folks, this can happen to anyone, just retrace your steps and make sure you've got it right.
As for the compromises you make building an X99 Hackintosh versus buying a new Mac Pro (the design of which is almost four years old!): 1. Wake/sleep just doesn't work on an X99 cpu/build. This has been mentioned in numerous posts. If ever Apple supports X99, that may change. It also may change if someone brilliant comes up with a work-around. To the best of my knowledge, that hasn't happened yet. 2. Slow boot - the 20 second delay is really necessary. I think some folks just skip this, and that will also cause a boot failure. Those bios settings are critical, not only in the bios but in Clover. My system still boots faster than a real Mac Pro, even with the 20 second timeout. 3. Thunderbolt. Thunderbolt is a pain in the a**, but if you use your system as a DAW, it's required, I get that. I don't need it, but if you do, I would only setup my system board and cards exactly as Giacomoleopardo's guide has stated and use only the card he used, which is an Asus Thunderbolt II card, not a Thunderbolt 3 card. I tried the Thunderbolt 3 card and it didn't work. That may be my fault, but the signature build for this motherboard and cpu was a Thunderbolt 2 card.
There just are some compromises that are unavoidable with a Hackintosh, but in my view they are minor. Folks like Giocomoleopardo and KGP should be lauded for posting!
I'm working on upgrading my El Cap build to Sierra and
@kgp I very much (!) appreciate your post!! Thanks again!