If you have purchased the NUC kit, the chassis is not USB 2.0 ready to use the internal header, this means that you will need to drill holes to the chassis and purchase one of the 2.0 mm USB pitch cable as the example linked below:
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Intel NUC Board NUC5i5RYB and Intel NUC Board NUC5i3RYB Technical Product Specification40Table12lists the connectors and headers identified inFigure10.Table12. Connectors and Headers Shown inFigure10Item fromFigure10DescriptionAAuxiliarypowerconnectorBFront panel connectorCSATA power connector(1.25 mm pitch)DM.2 2242, 2260or2280 (key typeM)connectorEFront panel dual-port USB 2.0 header (1.25mm pitch)FSATA 6.0 Gb/s connectorGBIOSSecurityjumperHNear Field Communications (NFC)VerticalFlexible Printed Circuitconnector(0.5 mm pitch
The USB 3.0 ports on the NUCs are fully backwards-compatible with USB 2.0 and USB 1.x devices. Unless you are already using all of the USB ports on the NUC, you shouldn't need to use the internal USB 2.0 header. In many cases, it's cheaper to use an external USB hub rather than a cable off the internal header.
In answer to your last question, the USB 2.0 interface utilizes only 4 pins; the fifth pin is an extra ground. On USB 2.0 2x5 headers (which support two USB 2.0 interfaces), the fifth pin for one of the two USB 2.0 interfaces is typically not populated and is used for keying (so you cannot put the cable on backwards.
Update Bios to 0032 or Latest, This adds the option to turn off USB 3.0
1. USB>EHCI to Disabled. changes all the 3.0 ports to 2.0.
2. Install Windows 7 normally and all drivers.
3. Set up remote desktop and test connecting to it.
4. Enter BIOS turn USB 3.0 back on, save and boot system your mouse and keyboard will not work.
5. log on to system with a second PC using remote desktop, install the USB3.0 driver for Windows 7
6. Your mouse and keyboard should now work.
Intel NUC motherboards with a 1.25mm pitch USB header
The easiest way is updating the BIOS to the latest, once updated load defaults and then go to Advance, then under USB, go to USB Configuration and disable the XHCI option. then follow this link Intel® NUC — Operating System Installation