I have d5 and you can deffo tell when it's been increased in speed. You could try running a little loop out of the system with just the pump and a small res etc and see how much it's actually pumping, at least it'll rule out a faulty pump.
I got in touch with XSPC, the lad there reckons I need two seperate loops, running two D5's. One 360 for the CPU, and then another 360 and a 140 for the two cards.
I went for a 2nd opinion
I think I have been the unluckiest first time watercooler in the history of the forums. Here's hoping the rest of the process goes relatively smoothly.