First off are you sure this is not just a misprint in the manual, the photos i'm seeing of the board show a connector with standard-sized pins in that position (though without the outer plastic part that the other headers have).
If it is real then it is just plain strange. 2mm square pin headers do exist but I've never seen anyone use them for USB 2 before.
You will probably be able to buy a suitable connector shell and pins from an electronics distributor like Farnell, RS, Mouser or Digikey but then you will need the crimp tool to attach it to a cable and it all gets a bit costly for a one-off. Also shopping for connectors is a PITA, every manufacturer names them differently. I find the best way to shop for connectors is to use the parametric search on a suppliers site (mouser, digikey, farnell, RS etc), select the pin spacing, number of pins and number of rows and then look through the pictures.
I'm referring to USB 2.0 headers with 9 pins. Some of them have a pitch of 2.54mm whereas others seem to have a shorter distance between pins equal to approximately 2mm. – xanz – 2016-06-29T12:43:07.937
Ah-ha. You could've made that clearer in your question, or I simply misunderstood it. Sorry, my answer then is irrelevant. – user1016274 – 2016-06-29T13:07:29.857