Afaik even corsair recommends to install the CPU cooler the same way as on OP's picture, not sure why but I say dont worry about it as the two 140 mil fans can suck all that heat away and that might be the reason for it, so that heat goes away faster.
( I'd just set them to be barely audible as their outake should be really ever sufficient )
F - I'd turn over the supply ( fan up ) so that the PSU fan helps to deliver some of the air to the GFX fan.
Wouldn't worry about heat from PSU as i have the ''same'' - Corsair HX, only 750W.
It depence how you stress your PSU but I doubt you ever do with 1000W supply, OC'ed CPU and one GTX580...
My point is that (over)sufficient PSU doesnt need to try too hard and thus stays cool at all times becouse its not stressed too much.
I'm however not saying that overkill PSU is always the best choice
At this stage though I recon swaping the airflow of C, as in my exp. (at least on my PC) most of the dust is getting into the PC trough the front.
Main point is to draw the hotter air outside the case, away from PSU and GFX.
The GFX getting cooled OFC by its fan but the hot air would get stocked inside of the card and thats why it has additional breathing room on each side of the card, left and right, to get rid of all that unwanted hot air.
That is why i recon moving the C fan little more up, so it can suck air from GFX on the inner side and OFC reverse the flow to get out, not in.
Also make sure your HDD is not in the middle of the C fan but perhaps at the bottom edge of it.
(looks like you'e done it that way, cannot see it properly

)