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WRT front IO connectors... I realised that the yellow USB header controls 3 USB ports instead of the regular 2, but I still have not figured out the pinouts

I think I have the pinout! My buddy has a Z600 with the same connector and he was nice enough to take a multimeter to the USB ports and the connector:

That's good news. So from that it appears that HP's colour coding is:

Red = VBus (+5V)
Black = Ground
Green = D+
White = D-

Your diagram needs to be flipped to visualise it directly on to the motherboard header because pins 1 and 2 on the left of the yellow header are 5V (Red B/Red C on your diagram).

You are correct that it is mirrored - I assume my buddy laid it out in order from looking straight into the plug itself when it was disconnected, which would make sense since the plug is mirrored from the header on the board.

I am going to order some of my parts to start on the project today - when I get it all going and can verify the pin outs I will clean up my diagram for the motherboard side. I'm so excited to get this started! 

WRT front IO connectors... I realised that the yellow USB header controls 3 USB ports instead of the regular 2, but I still have not figured out the pinouts

I think I have the pinout! My buddy has a Z600 with the same connector and he was nice enough to take a multimeter to the USB ports and the connector:

So technically there are headers on the board for 6 USB 2.0 ports total... 1 normal 2-port header, a 1-port header, and the yellow one has 3 ports?

I also have a USB 3.0 card I plan to use as well for my USB 3.0 card reader... of course that depends on the case I get. I need 4 5.25" bays and a 3.5" bay and I am having trouble finding an HPTX case that can fit all that. The DS6 can handle 4 5.25" bays, so I might just forgo the card reader since I don't use it as much as I used to.

(Edit: I lied. I found a few just now on Newegg. This one looks the best - http://www.newegg.com/Product/Product.aspx?Item=N82E16811815046&cm_re=HPTX-_-11-815-046-_-Product)

Or..... perhaps I should just fab my own case instead? 

(btw this is Stephen from the comments section on the article - just trying to get all the technical stuff down before I start buying parts)   

WRT front IO connectors... I realised that the yellow USB header controls 3 USB ports instead of the regular 2, but I still have not figured out the pinouts

I'm confused about the USB headers on the motherboard. Are the two (well, 1 and a half) blue ones (P26 and P27) to the left of the yellow header not standard USB? Or are we trying to get more USB ports out through the yellow header labeled P24?