This is going to sound a bit odd but the answer actually came to me in a dream last night. In the dream I remembered I'd had to disconnect the molex to pass the cable back though to the front of the case. Obviously my subconcious had been asking the question 'Did you turn the molex upside down by accident?' because in my dream I changed the pin locations and it worked. Woke up this morning, had a shot with the multimeter and what do you know, I'd connected it to the 5V red line. Absolute noob error on my part there.
Thanks Diablo you were right about the use of a multimeter but my subconcious beat you to it. Perhaps I should sleep on problems more often?
Edit: One small issue though, I changed the fluid to PrimChill Pure and with the shorter loop and new arrangement the flow speed seems to have increased dramatically, I'm not sure if it's the new fluid or the combination of the two but even after bleeding the system as much as possible and slowly pulsing the fluid through I'm beginning to get foam in the res. Problem is the higher flow rate means although the XPSC res has a tiering system which appeared to trap air bubbles before, now they are just getting pulled right back through. I know air bubbles are bad for performance so I'm assuming (as foam is effectively smaller air bubbles) that this is also has a negative effect on performance.
Like I say the previous coolants never showed this trouble so have you had any trouble with this before or is this just a dodgy coolant? If you have any clue as to how to remove the foam I'm all ears. Currently the rig is propped up to try and pull the air towards the front of the res.