Thats a bit weird, I am still confused as to why mine is working
This stuff gets weird sometimes.
I should clarify that when I say I tried the safe defaults, I tried them along with the required settings from the guide (i.e. VT-D off) and they still didn't work. For me the safe defaults set a higher CPU multiplier but disabled Turbo for a lower overall top speed. I think the BIOS was showing 1.6 gHz or 1.9 gHz max.
I deleted the file to disable wifi but the wifi is still working but it boots now, the update worked ok, and everything seems to work, although I do get the ethernet sleep issue.
They might still be cached?
You can try to replace Intel1000e kext in /EFI/.../10.11/ with the one of
post #56/59
You can also move the kext into a folder where it isn't autoloaded (I use /testing/drivers), load it manually afterboot (sudo kextutil) and then unload it and reload it (sudo kextunload then sudo kextutil) after wake to get Ethernet back. There's probably a way to script this but I haven't bothered yet.
So, I have two of these NUCs and it turns out they are from different manufacturing runs. Interestingly, only one will handshake with my AV receiver (Denon 3311ci) over HDMI. The NUC made in November of 2013 detects the receiver, but won't activate the display or pass audio although its HDMI works fine with a HP2159 monitor (display and audio). Even setting overrides in SwitchResX didn't help.
The NUC made in March 2014 works with the receiver. All BIOS settings identical. Same cables. Same SSD and RAM used in both. I even swapped the installed SSDs to make sure the problem was in the hardware and not the install.
So either the earlier NUC has some weird defect or there are some minor hardware differences between different manufacturing runs of the D54250WYK.
While I was troubleshooting I took one of the NUCs out of its case. The system runs way, way cooler naked. I'm considering drilling some small holes in the top panel over the fan intake (which faces the top panel) to allow more, colder air to move across CPU heat sink. I've also noticed that even in its case, the NUC runs cooler stood up on its side to expose the bottom vent. With improved airflow it might be possible to increase the power to run the cores and the graphics at full speed all the time without the fan going nuts.