Hi,
I know I'm rather late to this thread! Firstly, well done getting to the bottom of the problem. As I was reading I was thinking it must be some flow issue, likely pump...it was nice to see you got there too!

I actually tested my loop while flushing it out, so clean deionised in > loop > bucket so I could see that the flow was excellent.
I would like to comment however on your initial setup using parallel flow on your GPU's. I'd not expect you to get the best temps out of that, as you had it configured a little wrong. To get parallel flow to work at its
best you need the in and the out to both be in the top or in the bottom ideally - just my observation from much playing/experiementing.
In my own rig, the coolant comes in the TOP into the first card and through the second, before exiting once more via the top card and on to my CPU. Obviously as it's
parallel flow, roughy half the collant that goes in the top card exits out and up, whereas the half that enters the lower card (not getting heated by said card of course) has a near straight line exit back out again.This setup works very well.
I will say however - indeed I said it in another thread - those metal adjustable SLI connectors are really quite restrictive. I've compared my Phobya SLI connectors vs. some smaller flexible pipe and the latter wins. The adjustable connectors make a far neater build for sure, however my first GPU might hit 38c during extreme benching, the 2nd GPU will be 4-5c higher than that consitantly. Compare this to the smaller hose (I use 1/2" ID throughout my system
except for these smaller bits of hose) and I see 38c of BOTH GPU's under the same conditions.
As the flow is parallel overall flow is just fine, water will find the easiest way, and the loops does work just fine. However my imbalanced temps do bug me a little.
Note: serial flow works just fine of course and your temps are particularly close anyway so that's great. Personally, for my first WC build, I was keen to play around with parallel flow as I thought it quite an elegant solution. It's just a shame those SLI links cannot be had in a larger diameter - ideally 1/2" like my tubing.
I will add that my loop in near silent, as I'm very much with Tom on that side of things. Likely I could improve my cooling with the addition of a bit more noise, however, considering I rarely go more than 20c over ambient on the GPU's and 30c on the CPU, well, I'm fairly content in that regard. Oh, I thought my LAPTOP had a problem as the thing seems quite noisy now - silly I know, but true none the less!
Anyway, I think you've had your baptism of fire..erm, water now, so can enjoy your rig with the satisfaction of a job well done.
Cheers,
Scoob.