You won't even need the PhysX card with 3 GPU's in SLI, anyway. You wouldn't even need a dedicated PhysX card, period, but absolutely not with 3 cards in SLI. It would just sit there doing absolutely nothing.
Just forget about the PhysX card. That takes us to 4 PCIe cards.
With that said, because of the PCIe SSD (still a lot of bandwidth needed because of the 3 GPU's hogging a major chunk of it), I think X79 is the way to go, yes.
I think it's overall a huge waste, but if you can get a 3970x (are you sure it's not a 3960x?) for free basically, it doesn't even really matter.
Even it is a 3970x (which was just announced, apparently), there's no need for it. A 3960x is basically the same CPU, just clocked 200Mhz lower (which you can easily OC the 3960x to make up for it).