Yeah, so i think that 2 drives might be too hot if not cooled properly. I was browsing and found that Koolance makes a niffty little watercooling kit. It is outside of the case (I measured and you can fit it on top of a shuttle case with maybe 10 cm of the end hanging out, which i find acceptable). Then since everything except the tubes go inside, there'll be plenty of room. They also make a 2 harddrive cooler that fits perfectly between two drives. I think i'm going to do a little more research, but probably end up getting that for my SATA drives.
btw, the Koolance can be found here: http://www.coolerguys.com/productslist.aspx?categoryid=165