That 1000W SuperNova will actually be enough to run your system with 2-SLI 980Ti setup. I think you could get away with as little as a 750W PSU, although I wouldn't buy anything less than a 900W just to be sure.
Heavy video encoding and graphics would always benefit from a second GPU. Paying extra for a 1000W PSU now lets you enjoy the PSU now while also defraying total costs if you (or another owner) should ever choose to upgrade the GPU(s) later.
If you're absolutely set on a single-GPU system then you might find a Z97/i7-4790K/DDR3 platform is somewhat faster and cheaper. The most compelling features of X99 are 8 (or more) processor cores and up to 40 PCIe 3.0 lanes (which mainly benefits multi-GPU rigs), so the only real advantages of X99 for you would be buying into an upgrade path towards more CPU and GPU cores than Z97 can support.
I wouldn't really worry much about "future-proofing" because I think DDR3 is going to be around with the same capacities and speeds (and chips) as DDR4 for at least a few years since nobody will stop making and selling it as long as people keep demanding and buying it, while Z97 will not become obsolete unless/until an X99 (or later) chipset supports a processor which rated for truly faster and better performance in every measurable capacity. X99 is a fine way to go, but Z97 is still the better (and less costly) choice for most people.
Some data demonstrates that an AMD FX-9590/R9 system can actually outperform an i7/NV system for video transcoding tasks. But I suspect this is a temporary situation, caused more by fixable bugs in NVidia firmware and drivers than on raw AMD technological superiority (since, of course, AMD GPUs have technically inferior specs and capabilities).
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