Dgtal

The 980 is going to be better at DX11 tittles, but, overtime, nVIDIA will stop giving it drivers support (that graphics card came out 2 years ago while the RX just launched, so, withing a year, I foresee the situation with Maxwell to be the same as with Kepler), not to mention its already missing Async compute. Another thing worth mentioning is the performance gains in lower level API's that the GCN architecture is experiencing, like with Vulkan in DOOM while using Async the RX 480 surpasses the GTX 980 and places itself just a ~20% lower than the GTX 1070 (Vulkan gets rid of AMD's own "bottlenecks" and boosts performance quite a bit when having closer access to the hardware without having to deal with drivers as much). A safer bet is to go with the RX 480, but wait until the non-reference models come out.

Obviously, that AMD APU is going to bottleneck the hell out of the GTX 1060, so thats a no-no. Just go for the intel build. Also, I would first wait and see what the RX 480 does against the GTX 1060 and then decide instead of going straight for a GPU we know basically nothing about at the momment.
 
Edit: typos corrected.

Obviously, that AMD APU is going to bottleneck the hell out of the GTX 1060, so thats a no-no. Just go for the intel build. Also, I would first wait and see what the RX 480 does against the GTX 1060 and then decide instead of going straight for a GPU we know basically nothing about at the momment.
 
Edit: typos corrected.

change the cpu to an i5 6400/6500 and h110 board and a g.skill aegis 8gb, and get a better psu to save some money.

The 980 is going to be better at DX11 tittles, but, overtime, nVIDIA will stop giving it drivers support (that graphics card came out 2 years ago while the RX just launched, so, withing a year, I foresee the situation with Maxwell to be the same as with Kepler), not to mention its already missing Async compute. Another thing worth mentioning is the performance gains in lower level API's that the GCN architecture is experiencing, like with Vulkan in DOOM while using Async the RX 480 surpasses the GTX 980 and places itself just a ~20% lower than the GTX 1070 (Vulkan gets rid of AMD's own "bottlenecks" and boosts performance quite a bit when having closer access to the hardware without having to deal with drivers as much). A safer bet is to go with the RX 480, but wait until the non-reference models come out.

Windows 8.1 is better than Windows 7, once you get used to it you'll likely like it more. 
 
Change is good, you don't have to stick with Windows 7 your whole life.