I hope you could test the connector pitch using a USB header before ordering your parts. Unfortunately, as a software developer, even though I usually work in low level things, I have no idea of the inner workings of the detection or retasking of the connectors at the hardware level.
In fact, I was hoping someone could answer my question on rewiring the header internally, which by the way, seems to be in the same line as yours ( http://communities.intel.com/thread/42636 ). I think it's more probable that you have an answer to my question, which I'd really appreciate. Best regards,
Miguel