On the regards of the PCIe 3.0 part of your post. That is just a bandwidth number. Therefore all GPU's regardless of what PCIe 3.0 or 2.0 it says it supports should be interchangeable. You will only notice a minute difference in performance between 3.0 & 2.0 (we are talking milliseconds here) so as far as that goes you should be fine.
Another thing to consider is you don't want to bottleneck your APU. So I wouldn't go above a GTX 780 Ti. Though when you install a GPU in tandem with an APU the integrated graphics part of the APU should cancel itself out an only the GPU will be handling graphics as you will be plugging your monitor into the DVI, VGA, HDMI ports that come with the GPU. This is of course as long as you are running a single monitor setup.
Most people always install an aftermarket cooling solution regardless of rather or not they plan on overclocking or not because the stock heatsink is usually crap an is only optimized to just barely take care of the heat disappation from the Processor.
If you are referring the the heat within your case than I'd suggest making sure your motherboard has the fan power connectors for you to install extra fans for extra internal cooling of the case. Though a GPU will have it's own cooling solution, different from each manufacturer (EVGA, ASUS, MSI, NVIDIA, AMD, etc...) so some research is in order. Though if you don't really plan on overclocking your setup it isn't really too big an issue. Use the onboard suite to check temps if you are concerned.
With all that said looking at the parts you've picked I don't see any reason why this wouldn't work out just fine for you.
Edit: Your Ram may be a slight overkill. 2x4gb 1866mhz running in dual channel should be enough unless you plan on doing more than gaming. In which case I'd have said go with Intel if doing video rendering or anything other than basic computer use an gaming.
AMD + ASUS = Good Machine