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I'm kind of forced to run my 6990 in the primary slot due to space and a pci soundcard but, after having it like this, I think it's the best configuration. With the occasional game that has problems with trifire, there's a good chance the 6990 will still run it on both gpu's giving better performance than running it on the single 6950(70). Of course when crossfire won't work at all, it would be better to be running it on the 6950(70) then due to temperatures.
Great article.
No problems with 6990+6970 here mate. What PSU are you running? Also, I wo;ld suggest the 6970 goes in the first PCIe slot