PCIe 2.0 isn't going to bottleneck a card like the GTX 970, nor even the latest Titan XP. It's not like you can just 'enable' PCIe 3.0 technology... either the hardware supports it or it doesn't. Honestly, any performance jump from 2.0 to 3.0 is negligible, maybe even within the margin of error. An M.2 drive might theoretically be a bit slower on 2.0, but you probably wouldn't even notice it.
The only reason you might be seeing a flat 60 FPS in every single game is if you have VSync enabled in your graphics settings, which caps the frame rate to your monitor's refresh rate (60Hz).
The version of DirectX a game uses is determined by the game itself (usually just 11 or 12 for newer titles), whereas System Information shows DX12 because that's the highest version your system supports. Personally, I'd stick with DirectX 11; Nvidia tends to perform better in DX11 most of the time, and let's face it, DX12 isn't always the best-optimized version in many games.
Yikes... that quality is pretty rough, but since the AMD Athlon and RX 560 don't pull much power, I guess it might work for now.
Your processor should be fast enough to keep up with that GPU, though you're kind of stuck because there aren't any faster CPUs available for that specific socket on your current motherboard. You could try overclocking, but you'd probably need to grab a new cooler and a better power supply to go with it.
The RX 560D feels like a weird invention from overseas... I mean, there's an RX 470D that actually has fewer cores, so the naming convention makes sense there to differentiate them, but this is just an RX 460 rebranded, which seems kind of pointless. At least it's a bit cheaper than $33.
Everything looks fine, but you might want to try bumping the memory up to 2666MHz and setting the processor to 3.7GHz using the stock cooler. It’ll probably help you get more out of the graphics card.
Buying this CPU right now feels like a bad move; you could probably find something twice as good for the same price. There are definitely more cost-effective SSD options out there too.
Regarding shipping, it’s reliable enough, though I suspect you'll get hit with an extra 25% in sales tax and customs if it's coming from the USA 😬
Sometimes you can snag a killer deal on sites based in Austria or Germany that ends up being cheaper than local prices here. Where are you located anyway? 😛
For everything else, I'd suggest hunting down a used Intel Core i7-6700, 6700K, 7700, or 7700K; buying them new just doesn't make much sense. Intel basically retired those older platforms with the 1xx and 2xx series boards just a few days ago with the release of the Intel Z370 chipset and Coffee Lake processors.
Amazon has the R5 1600 back in stock for under $533 if you grab that PCE discount. I guess it might actually be the right time to snag that Asus on sale along with the processor over there... especially since the dollar has climbed about 20 cents over the last ~3 weeks 😁
I don't think it's worth buying those new 4-core i5 processors anymore😁 They just aren't a great value, and honestly, most CPUs don't really struggle on stock settings anyway.
Maybe just hang tight for a week or two. Once those new Coffee Lake chips drop tomorrow, people will probably start offloading their Skylake and Kaby Lake i5s and i7s. 😉