Just an update on the GHR-03V-S connector, I ordered some and they finally arrived, so I can confirm that this is the appropriate connector. So you should be able to replace a fan's standard connector with this one and it should work fine. As for how to actually turn on the port for the fan, I haven...

While I don't know about your particular use case, you could use pin 4 and 6 from the 40 pin gpio for a simple 5V fan. However, I am also trying to figure out the male connector for the fan header, so I can't offer much more assistance than that at the moment.

Not sure if you are aware, or if you already ordered it, but it appears to be available now in the Matrix Accessories category.