According to the below image I am inclined to say yes I can. As the GPUs x16 lanes gets handle by the CPU (i7-4790) and the USB expansion PCI is handles by the Z97 chipset and not the CPU.
Yes you won't be infringing on the x16 slot (though even if you were it wouldn't be an issue). The x1 slots are separate from the others as they are handled through the chipset and the graphics slot is handled through the processor (according to the diagram you gave at least).
Thank you so much for the answer. That is what I thought, but when I see several people on sites like toms say otherwise I got nervous. So I decided to come here and get the real scoop.