I dont know if you have sorted your noise problems out or not but i thought id add my 2p's worth. I was on the same mission as you a while ago now, to reduce the noise of my system as it was unbearable. The main source of the noise in my system was the GFX cooler, it was a 40mm little blue led thing that whined away at 4000rpm
and the gpu was still reaching 90oc under load. I installed an Arctic NV silencer and i have never looked back, very quiet and my load temps are now 50oc
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Case fans can be tamed by 5volting them as i have done, there is a good guide on how to do this here
http://www.dslwebserver.com/main/fr_index.html?/main/5-7-adapter.html
also using rubber shock absorber mounts like the ones pictured below can make a big difference. if youd rather use the fan gaskets you can buy these arnt as effective but help to seal the fan to the case. If you are going to use a gasket instead of the rubber mounts then id reccomend the Acusti gasket, its dearer than the vantec gasket but is softer, 2.5mm instead of 1mm thick, and also has better screws and rubber washers included.
A hdd enclosure made a big difference to the seek noise of my hdd and also the general humming sound it made. I also put little ultra soft rubber feet on the enclosure and put it onto the bottom of my case, i cant hear the seek at all!, and the front fan still helps to cool it, im getting 22oc idle temps.
Mark