The media cache drive is a bit small. 256 GB might be better. Definitely the Noctua cooler.
Corsair Hydro coolers do not give better cooling performance than air coolers from Cooler Master or Noctua, nor do they run quieter. They are only more expensive. Don't forget that air coolers in push-pull configuration have two fans, that are replaced by two fans on the radiator when using a Corsair Hydro. Unfortunately, the Corsair fans are pretty noisy, thereby defeating the intention of water cooling to make things more silent. Effectively, one replaces two fans with an average noise level of 25 dB with two radiator fans with 35 dB. If the cooling performance was better, that extra noise might be overlooked, but that is not the case. Up to around 4.8 GHz overclock, the performance difference between air coolers and Corsair Hydro is negligent. So, if you opt for Corsair Hydro coolers, you don't get better cooling, you do get more noise, more power consumption (because of the waterpump) and you spend a lot more.
Okay, that's what I thought, but do you think that particular Noctua cooler would be effective enough? I really don't understand the compatibility of most coolers with various parts of computers.
And I'll take your advice on the 256 GB media cache drive. Other than that, any other suggestions?
Looks good, but if you are worried about the cooler, also consider the Noctua NH-D15. Just check that it fits in your case.
I wouldn't really know about the Noctua coolers as a whole, because they're too noisy for my taste but in general it's a solid brand. Don't take the cheap water cooling kits and even the expensive ones will likely only be on par or slightly better (allowing maybe 100 Mhz higher clockspeeds) at the cost of being excruciatingly loud.
One thing I do notice is the Gigabyte motherboard. I've read that the whole range of Gigabyte X99 motherboards had some serious issues. They can probably address those through future bios update and maybe it's already happened. I think the first bios updates were meant to help but didn't fix as much... Unless you have a keen brand liking to Gigabyte I would suggest looking at Asus, MSI or even Asrock, however if you really wanna go with your first choice then at least check and make sure they've worked out their issues!
Last note, did you consider looking at any M.2 or even pci express ssds? I only thought of those after I ordered my own parts last week, but my budget probably didn't have room for them regardless, however you're spending a good chunk of money on ssd's and a faster ssd might be welcome to you.