I had to go back threw the thread, look at pictures, then go find a few pics of your case to familiarize myself with the airflow, and fan useage/size.
First, glad to see you used a 120mm fan on the rear i/o panel and that it is blowing out. Not sure what you are using, but you may want to go with a higher CFM fan, such as a [url=http://www.scythe-usa.com/product/acc/002/sflex_detail.html[url]Scythe S-Flex[/url] med or high speed
Second, the fan in front of the hard drives. This fan should be blowing in, and can be a low cfm fan. To high, and it will be noisey. A [url=http://www.noctua.at/main.php?show=productview&products_id=9&lng=en[url]Noctua NF-R8[/url]would be perfect here (quiet).
Third, the "case side" fan should be blowing in; and again I would use a low or medium cfm fan (quiet).
Fourth, that fan duct! hopefully it's fairly close to the HSF. That is when it is most benificial. Because you do have such a large graphics card, I would get a mount, and use a fan parallel to the motherboard, blowing down on the memory, etc. An [url=http://www.antec.com/us/productDetails.php?ProdID=75018#[url]Antec Spot Cool[/url] is the perfect fan for this setup. If the proper setup cannot be found, my next resort would be to add a blow-hole to the right of the cpu duct, again blowing in with a low to medium cfm fan (quiet).
OK, enough rambling now and sounding like a college professor!