The 900D is GREAT. Just impossible to lan party with unless the party is at your house. I do, however, agree the case screws are a bit tough to get used to.
Anyways, do you have a custom fan profile set on MSI Afterburner? You can make your own profile to aggressively up your fan rpms and enhance cooling. Also install top fans (if you dont know how the top mesh slides off towards the "open" side/ left when facing the front) and have them ramped up for aggressive cooling. You should have top fans first for the one massive reason... heat RISES. You could also rig a 120mm or so fan near the backend of the two cards with zipties to have direct airflow on them. And this goes on, I apologize as i have a 900D and have had a heat suffering 7970ghz, try taking the front metal panel (the one that says Corsair on it) off. I've found that significantly helps temperature wise (3-5 degrees C). Try spacing them differently if you have the extra pcie lane and a longer x-fire cable. If its the bottom card that is now hotter (due to switching) buy a slot fan such as:
http://www.newegg.com/Product/Product.aspxItem=N82E1683...
Thats about all I can suggest unless you want to really butcher the 900D.
Aaron