X16 x8 x16 motherboard
Looking for a motherboard that supports 1366 chipset ddr3 ram up to at least 1600 and has a pci-e configuration that allows for split sli running at 16x for both slots. so x16 x8 x16 so cards are split and get more airflow.
This is your best bet... Gigabyte GA-X58A-UD9.
With current gen graphics cards, you are only seeing 2 to 5 degree temp increase when run in pairs with no open slots. It isn't a major issue, so don't be to concern... IMO. I would look at the ASUS P6X58D-E, as an alternative.