I'm having roughly the same problem but in my case it's because I installed aftermarket Arctic Cooling fans on my 6950's. It will leave so little room between the upper card and the lower one.... I'm also worried about temps, especially on the upper card.
I added a 120mm fan to the side of the case ( to blow onto them) and even added a custom VRM cooler (with a 80mm fan) to the upper card. Normally I wouldn't worry about a dedicated VRM cooler but I'm hoping this will help keep the upper card, closer to the temps the lower card will be at.
I'm thinking of running both GPU fans at 100% initially then see just where I'll need to put each of them. They are quiet enough, so noise wont be an issue for me.
Have you looked into an aftermarket cooling solution for your 5800's? My single 6950 went from sounding like a vacuum cleaner to so nice and quiet...well worth spending a few bucks, for the mod.
But again, like I too have.... the space between the two will be a factor for you as well. That really looks tight in there.
Edited by OldtimeGamer - 7/16/13 at 11:21am