Unfortunately (for me), I found the computer out of sleep this morning, waiting at the login screen (lock screen, not a cold boot login). Upon logging back in by USB audio device was missing, and wifi wouldn't turn on. It also got stuck rebooting. All in all, a bit of a failure :¬)
Well that didn't work out as planned. Go into System Preferences/Energy Saver and remove the tick box for Wake for Wi-Fi Network and Ethernet. The only selection I have ticked is put hard disks to sleep when possible. What Wi-Fi card are you using? is it a USB Wi-Fi card by any chance.
I use USBInjectAll.kext and all of my ports work. When I originally tried the longer method some ports stopped working. I must admit, although being quite a technical person (ex-programmer), I find the DSDT and SSDT tweaks quit daunting, I can't seem to grasp them fully.
What would you recommend?
Seems as if your USB's aren't working quite as they should. Your USB audio device wasn't connected/ejected after sleep.
Credit RehabMan documented by ammulder:
RehabMan doesn't recommend using the raise port limit patch permanently with USBInjectAll.kext. The idea is get all your USB ports recognised when USB2/3.0 devices are connected, to document what header and port your devices are connected too. You can inject this either by SSDT - which will inject only the ports you use/have connected for use or with USBInjectAll.kext and a boot flag called -uia_exclude_(the ports you don't have connected/won't use), this will stop USBInjectAll.kext injecting those ports.
So an example would be USB2.0 ports are HSXX and USB3.0 are SSXX, if you didn't want to inject ports HS03, HS08, SS13, SS18 your boot flag would be -uia_exclude=HS03,HS08,SS13,SS18. The idea is getting your working ports down to 15. This is Apple's limit, in return you can remove the raise port limit patch, remember USB3.0 counts as 2 ports and USB2.0 as 1 port. You've got 6 USB3.0 and 8 USB2.0 - Total : 20 Intel ports.
To find out what ports are connected you'll need a USB2.0 and USB3.0 device/thumb drive and IORegistry Explorer located at the bottom of Post#1 here
[Guide] How to Make a Copy of IOReg | tonymacx86.com Search>XHC, you'll see the device and what port it is connected to in IORegistry Explorer.
ammulder has written a great guide on how to put an SSDT together and how to go about finding which ports you've got connected for use here
10.11.0-10.11.3 Skylake Starter Guide | tonymacx86.com Step7 onwards. I've also documented how I did this in my build description linked in my signature under my Skylake build.
Obviously this is entirely up to you. Looking at your system specs here under USB
https://www.asus.com/uk/Motherboards/MAXIMUS-VIII-HERO/specifications/ you also have 2x ASMedia USB 3.1/C&A ports on the rear of the motherboard, these are controlled by the ASMedia controller and won't count within the Intel port limit.
Unless you've installed GenericUSBXHCI.kext(3rd Party USB driver) I guess these are not working for you.