I disagree on the 6990. Though it'll be cheaper to cool (really just the added cost of a single waterblock), it won't necessarily warrant better performance.
You still need to use Crossfire drivers because the PCB has two GPUs onboard, so your argument there is moot. Also, it has been proven time and again that 2x6970s > 1x6990 in graphical performance, and every little bit counts with 3 monitors.
(Double the 6970 results; the bench list only has 1x6970 - http://www.anandtech.com/bench/Product/515?vs=509)
Since the 6990 uses two of the same GPUs in the 6970, the heat load will be about the same, so the hardware setups should be nearly interchangeable with the cooling setups. You might need a bit more cooling with the 2x6970 setup, but as long as you have at least 480mm of rad space you should be good to go. My 2x6950 2GBs ran at 45C while gaming and I had my 2500K in my loop with a 360 and 120mm rad with 110CFM fans.