I've been searching high and low but cant find what I'm looking for, I have made a (poorly sketched) mock-up of what I am looking for below. Any help would be greatly appreciated.
(not quite sure how to insert pics)
Would this
and this
http://usb.brando.com/usb-3-0-20-pin-female-header-90-deg-_p02545c067d015.html
solve your problem ?
Would I be able to plug the blue header directly into the female connector? I'm trying to keep the USB 3.0 cable as low profile as possible.
To be honest I wouldn't know. I don't know enough about it to answer your question. I did some hunting around online for what you are after and that was what I found.
A lot of other forums that have the same question say to get a extension cable like this http://www.ebay.com/itm/20inch-USB-3-0-Motherboard-20-Pin-Header-M-F-Round-Extension-Cable-USB3-2020-/280801382782?pt=US_USB_Cables_Hubs_Adapters&hash=item416111117e
but I don't think that it is as low profile as you are after.
Sorry I couldn't help more