If you remove the hard disk drive the gigabyte should fit. But it can be very tight. Why do you take an overclockable cpu and a h97 mainboard? Doesnt make sense. Whether you take the non-k-version of the cpu or a mb with z97 chipset.
But back to the gpu: if its between gigabyte and msi, I would take the msi. A little bit less noise, less heat, shorter card and as powerful as the gigabyte. And it looks nicer (but thats only my opinion)