You are attempting to compare two different measures.
Memory frequency of the video card can be measured in Ghz, more commonly in Mhz, though that is again a marketing ploy... Really it is GDDR5 and it runs at half that speed, but has throughput on both the leading and receding edge of the memory clock, so the effective speed is greater.
a PCIe 2.0 x16 slot has a theoretical throughput of 8GB/s
a PCIe 3.0 x 16 slot has a theoretical throughput of 15.74 GB/s
R9-290 has a bandwidth of 320GB\s across its 512bit memory bus. That is how quickly the card can move data within itself.
PCIe throughput determines how quickly the rest of the system can get data to the GPU. You won't notice a huge difference between PCIe 2.0 and 3.0 with a single GPU.
H97 board will also allow you to upgrade to a Broadwell CPU when they come out. If you so chose. Should also have a few nicer features that you might want. Extra USB 3.0 ports, crossfire support, More internal sata ports.
Stock cooler can be a bit noisy during heavy processing, but it is adequate for keeping the cpu cool.