I installed Windows, then the motherboard CD. The keyboard and mouse work in BIOS and were working up to a point. I have a Corsair K70 keyboard and a Razer Abyssus mouse. I shut the computer down, unplugged them and plugged in a Microsoft mouse and keyboard, still nothing. They still work in BIOS just fine.
BIOS version is 1.16, X99 Classified motherboard.

That's the issue. I no longer have keyboard/mouse control in Windows. I can't do anything. Looks like I'll have to do a reinstall and only install the network driver, then download the other drivers from EVGA.

HarryD
Downloading the files manually. When I click "download" for the Intel ME file, the browser just goes back to EVGA's home page. I'm using Safari 8.0.4 (MacBook Air).

Yeah, not sure if the site is compatible to Safari but my guess is it would be so.
 
Make sure its just the keyboard and mouse you're plugging into the USB ports in the back and nothing else as there's a possibility of conflicts.

Also, clear your CMOS and if that doesn't work, remove and reinstall the CMOS battery if everything has been tried to this point.

After reinstalling Windows I installed:
chipset drivers, keyboard/mouse still work
network drivers, keyboard/mouse still work
USB3 drivers, keyboard/mouse do not work after restarting the computer
 
These drivers were from the disk. I did download the drivers from the website and saved them to a thumb drive. I guess I could try those. What I'll do now is install only the chipset driver and network driver then see if I can go to Windows Updates.

Computer is partially fixed. I installed the USB3 drivers from EVGA's site and I no longer have the missing keyboard/mouse issue.
 
Now I have a ! in "PCI Simple Communications Controller" in device manager. Does anybody know what driver I would install for that?

Glad it all worked out. 

HarryD
I'd still like to hear from someone that works at EVGA as to what the issue could be. Both the USB3 driver issue and why I can't download a certain driver (Safari and IE). 

 
What Driver are your looking for to use with a Browser?

HarryD
No longer looking. The only driver I'm installing from the website will be the one for USB3.
(Intel ME kept bringing me back to the homepage)

So then the USB 3.0 Driver on your Motherboard Install Disk is not working>?
 
At this point I think I would do a Fresh OS Install and install all the drivers from your Motherboard Install Disk.

HarryD
The drivers on the CD work except for the USB3, that's the only driver that breaks my computer. I don't know what version each driver is but on my next reinstall I'll use everything from the CD except USB3, that will be from the website.

Odd, I had now problems at all when I installed Windows 7 x64 and the Install CD

HarryD
I think I may have found the problem. If I let the CD autorun and install the MB drivers I have the no keyboard issue. If I manually install the Intel ME driver before the USB3 driver I don't have the no keyboard issue. I'll do more testing to see what's going on.
Anybody else running into this? I'd really like to hear from an EVGA employee on this matter.

True, that is why I use it.
 
"EVGA employee on this matter." I would open a Support Ticket and ask that question.
 
I will make a difference in the order of the drivers when you install them, this is not uncommon.
You can manually install the drivers, but you still have to install them in the correct order.