The 212 EVO is the most available cooler, and while it's not necessarily the very quietest (still better than stock), others like the Pure Rock are an absolute pain to install. I put a Cryorig H7 (better in every way but hard to find) in my i5-6600 non-K system, and even during an extended stress test, it remains inaudible and keeps my CPU under 40 degrees (~26 at idle, only a couple of degrees above ambient). And so this begs the question whether an aftermarket cooler is necessary at all. If you are going the "future proof" route and think you definitely might overclock at some point, go ahead and get the cooler. But otherwise, if you're never going to overclock like me, anything other than stock is wholly unnecessary - unless you really value near-silence at any load. Food for thought.
Do you mean Z170 Pro or Z170 Pro Gaming? The former is quite expensive for what it is, and the latter has more mixed reviews (Newegg). But to answer your question, no, there wouldn't be. I've heard that Gigabyte are the best, and just as an example, the Z170-HD3P is £30-40 cheaper than either Asus 'board, and has 1 more USB port than the stingy Pro, has equal or better 32Gb/s M.2 support... and generally the only difference is fewer expansion card slots. Ultimately, no motherboard will make any difference whatsoever to your framerate or storage transfer speed - what matters is the feature set you desire. Need x no. of expansion slots? Go for the board that has that number (or greater). Because you could always add more USB ports via a hub or SATA ports via an enclosure or expansion card or something, so it usually comes down to how many slots/lanes you need. Although that cheap Gigabyte board should probably be more than enough.
Have you decided which brand of 390 you're going for? I've also heard that Sapphire make the best AMD GPUs, but the Nitro 390 is also one of the longest, at 308mm. (XFX is 295, Asus is 300.) And the Cooler Master websites states for your case: "VGA Card length: 270mm". (It's also 5.5 years old?) You might want to think about another case if even the brands with 390s that have only two fans still won't fit. Hope this helps.
