Your 9-pin reader is perfectly fine to use. Plug it in all the way to the keyed side where there's only one pin, leaving the opposite two pins unused and exposed.
Starting at the keyed side and moving away, the next two are grounds. The next 4 are USB signals. The next two are 5V. The last two are a ground and a GPIO that we use to allow BIOS (and ultimately manufacturing test tools) to determine whether or not there is a device actually connected to this port.
This header can actually support 2 ports.
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