As a former enthusiast in the liquid and vapor phase-change cooling market, I can point out a multitude of things gone wrong here.
1) Single Cooling Loop - with 4 quad-core processors, this machine could net much better bang-for-the-decibel out of a dual loop system - one loop handling one pair of processors, second loop handling the other pair. Optimally speaking, a quad-loop system (individual loops per processor) would net even better results.
2) Video cards have fans, too! - Find yourself a video card that uses cooling pipes or similar technology, rather than fans. Those little fans spinning really fast make _LOTS_ of noise.
3) Speaking of noise - WD300 Raptors? Congrats, you just put the noisiest modern hard drives in a machine "built to be quiet" - if no expense was to be spared, why is this thing not outfitted with Solid State Disks???
4) Problems with the liquid - in addition to number one above, the reservoir is mounted at the bottom of the case? That's an amateur mistake right there. Reservoir at top of case = any air infiltration gets trapped at the reservoir. Additionally, the "angled barbs" are 90-degree bends - not exactly what you want in a low-flow system, backpressure is going to kill that pump, or at least cause it to whine incessantly, even at lower flow settings.
5) PSU - Corsair HX 1000W PSU - why not a PC Power and Cooling ultra-quiet unit, or a SilenX-modded solid cap PSU? Instead, they opt for a PSU rated at 57dBm?
Amateur job, Puget, very amateur. If anyone feels the need to build a super-quiet box, they really should shop around and look into these type of issue, or suffer sever disappointment.
E