Ah I see,
Well there seems to be some architectural issues that keep the drive from telling the machine that it's bootable when you are in PCIe 2.0 lane. I switched to the second 3.0 lane and boom, works like a charm. No improvement on speed though, oddly enough.
Looks like I have a choice to make here,
I can upgrade my video card in the future and just run 1 980 Ti, or change to the X99 platform to accommodate my PCIe usage.