them pumps should not be loud. Ive had Mcp350 3 mcp355 18w and 1 mcp355 12w amd a d5 not one has been loud. I have heard people have had loud ones tho. Have you got all the air out your loop.
What rad.s and fans do you have.
Ive got a 360 and a 120 with a 2600k and gtx480sli with temps about the same as you.
As for getting the air out of the loop, that's one issue with the CM 690 II, with the rad being at the top it's quite possible that air is collection up there. I've tried tilting the PC in all 4 directions and that cleared some, but it's hard to tell if it's cleared it all.
I've got an XSPC RS240 rad in the top (as I think it's one of the few that will fit) and an EX Coolstream XT 240 in the bottom. I will say to the OP here that with the RS240 I found it was a bit tricky to get the fan cables down past the rad (remembering they sire on top of the metal part of the chassis), I believe the Black ice GT stealth 240 rad might be wider which may cause more issues (but it may be fine, I've not tried one).
As for fans, I used the theory that everyone loved Apaches on heatsinks and Vipers are better than Apaches, so I used them on my rads. I've bought some Gentle Typhoons though, I just need to get around to fitting them.
I'm also hoping to replace my 4870x2 with a GTX480 in the hope that a single GPU will kick out less heat (I know it sounds silly expecting a 480 to be cooler than something, but...)
I'm not sure what CPU the OP has, but my worry (and this may be complete rubbish but seems logical to me) is that with the Phenom II having a max safe temp of 62ºC, I don't want to put in a graphics card that will kick out too much heat as this would surely affect the cooling of the cpu (i.e. if the 480 is running at 57ºC then surely that'll heat up the water more than the CPU and thus affect the CPU cooling.
For this reason I'm considering, much like the OP was, to go with dual loops to isolate the heat from the GPU. Since you've tried various pumps, how much difference is there between the 10W (MCP350?) and 18W (MCP355?) pumps? Is the 18W one worth the extra £5 (it apparently does 600lph as opposed to 400lph). Would this make much of a difference if each loop is only cooling 1 thing?
Hopefully some of the stuff I've mentioned/raised will be useful to the OP too (as I really didn't want this to be about me, but I'll take any opportunity to get a little advice/help. Sorry OP).