Aren't recognized or not working/don't have power? One of the wires could've become unplugged via shipping if it's a power issue (try plugging your phone into it and see if it charges).
 
Other than that, I won't be of much help. I DO know that for example when using an external CD/DVD reader/writer, I have to plug it directly into the back of the Mobo for it to work. It turns on with the top USB's but the recognition of the CD/DVD in Windows goes in and out (could be an issue with the device itself but haven't checked with another). Might just be how it's connected/wired to the Mobo from the case?
 
Also, for the temperatures, maybe try going to the temperature "Mode" on the front of the case until it goes to the Temperature and using the up/down arrows. I personally haven't tested this myself but there might be a list that the arrows will navigate (kinda like how they will increase/decrease the fan %). Why would you want F or K? The sensor on the front only shows the ambient case temperature AKA what your thermostat says (unless you get things really hot in the case and don't have the best airflow which is pretty much impossible with this one) so its use is minimal compared to a temperature sensor of the CPU/GPU, in which case the safe/max temps are all measured in Celsius anyways. With specific programs you can convert degrees C to Fahrenheit and I know that HWInfo64 shows both at the same time.
 
Ex: CPU Temp: 62C (143.6F)
 
Not sure about Kelvin though, unless you like seeing really big numbers

That's very odd.  I will say that I had some trouble with my USB 3.0 pins on the motherboard....the case cable would not plug into it at first, and sure enough the pins were bent slightly.  It may be worth taking a look and making sure it's not intermittently cutting in and out from a bent pin.

So I cracked open my case because I had to change out the gfx card because apparently, it was having a hissy fit when it came to Anti-Aliasing and would crash.
 
I checked out the pins on the mobo for the usb 3.0 and it looked like there is one missing from the bottom left corner? Not sure if it is supposed to be that way though since plenty of headers have pins missing from one spot.

Unless something got unplugged somewhere that I can not see, all the cables appear to be plugged in and seated firmly. Everything in the bios related to USB3.0/3.1 is enabled, but it also claims that there are two keyboards plugged in, despite only actually having 1 keyboard hooked up, and if I plug a USB drive into the ports on top of the case, it shows up just fine on the bios, however plugging the same drive into the front USB3.0 ports does not show up as a connected drive in the bios.
 

Hello everyone, I also find these same problems bengrimsbo, I did all the driver tests and does not change anything, I attached a phone to port 3.0 and reload as described previously by the user. So somebody have a solution?

turn Windows 10 Fast Startup OFF, when upgrading drivers, firmware or hardware
 
Windows Central - How to disable Windows 10 fast startup (and why you'd want to)