If it is literally a paper thickness between the frame of the fan and the RAM, perhaps you can use a filing tool to file away, say, 1mm of the frame material to allow some more clearance.
For testing graphics card, 3DMark 11, 3DMark Vantage, Heaven Benchmark...etc are fairly popular.
For testing HDDs, HDTune and CrystalDiskMark are both common tools.
Regarding the GPU air duct of the HAF932 Black Edition, I suggest you do not
use it. The duct (plus fan) is helpful if a graphics card uses traditional 'front-centrifugal-fan-intake-and-rear-exhaust
' cooling design. But your video card Zotac GTX460 does not use this type of cooling and it will expel hot air via its front. So, having the air duct will not help but might likely hurt the heat dissipation.
Lastly, I am glad that the CPU cooler works out OK.