I've had some success but still have a few things to work out.
Firstly, I've use continuity checks on my multimeter to determine the cable for each corresponding Firewire pin. The results I've put are below (please note most internet FW pinouts are of the cable view which is opposite to the jack view I am using):
The first surprise was that the 6 wire cluster was for the Firewire 800 port, and the Firewire 400 port appears to be using the 9 cable cluster. The second surprise is that as far as I can tell FW800 pins 5,6,7 & 9 don't seem to have a corresponding pin. I don't understand the distinctions between FW400 and 800 enough to know if this is surprising, but as far as I know two of these should correspond with the shielding around each of the two sets of twisted pair.
I'm confused by the manual's documentation of motherboard pins 7 (+12V) and 8 (+12V fused). If "fused" means an electrical fuse I can't see any indication of it on the motherboard or device side. If they mean fused as in "joined together" then I guess this is a reference to the two white cables that are paired.
Either way, I wasn't able to get headers of the type I needed because I live in a small town. I therefore removed the USB2 header plug and wired up the FW400 port per annotations.
It seems to work with an iSight and external drive - obviously only at FW400 speeds - but I didn't want to test too extensively given my confusion as to which of the Gigabyte Motherboard's power ports was appropriate.
I'm hoping someone who understands the FW800 pinout better will be able to give more information.
I'm presuming otherwise I'll be able to wire the port up like I've done with the Firewire 400, but that it might only run at the slower speed.
First off, be very, very careful as you proceed. there is voltage sent over firewire and a wrong connection could damage the board , the connected device, or even you. Just proceed very methodically and carefully.
i would completely disregard any cable color data unless you can get (and i suggest trying) a pinout diagram from gigabyte for this part (or probably more realistcly, find the motherboard it was meant to go with and use the manual of that board to read the pinouts). I will try to investigate this myself but a quick email to gigabyte might get the needed info. I just think the colors on that are probably non standard and a dead end. You will need to confirm the actual pinout of every pin, regardless of the color code.
Lets figure this out and i'll order myself a set of headers as well
Thanks for your help, all the advice is spot-on and I'm triple checking everything as I go.
I haven't had much luck with Gigabyte thus far. Initially I'd tried to order a motherboard bracket or get access to a similar manual and their service department has flat out refused to assist because I don't own a motherboard available for purchase off the website. Reasoning that this was a general enquiry (not a warranty claim) fell on deaf ears, and as far as they're concerned any motherboard missing the Gigabyte logo (as ours is) is a counterfeit and therefore ineligible for service.
Hopefully my additional headers come soon; I had to order from China - I live in a smallish town and my electronics shop only sells 5x2 IDC plugs suitable for use with ribbon cables.