The reason I got the RIVE was it's huge PCIe slot capability. I don't see any problems with your proposed array, the only card connected x16 will be the video card, but even it cannot fill the entire PCIe 3.0 bandwidth. I have a Noctua NH-D14 cpu cooler which is a monster and is very close to the backplate of the GPU. If you are in a similar configuration, just place a piece of non-conductive material (e.g cardboard) between the two and you'll be fine.
Also, remember to plug the 6-pin EZ-Plug on the motherboard. It is required for a stable input power if the slots are populated with power hungry cards (like a build with quad-SLI) and although only the video card is the only one with 100+W requirement, plugin it in won't cause any trouble.
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Rampage IV Extreme BIOS 4206
Intel I7-3820
32 GB Quad Channel Kingston Hyper X Genesis
2 x Nvidia GTX 690
2 x WD Velociraptor 250 GB RAID0
Intel 120GB 320 SSD
Noctua NH-D14 SE2011
CM Silent Pro Hybrid - 1300W
CM HAFx