EVGA Hadron Air Overheating

Right, I'm pretty sure that your issues are caused by several issues and it's possible the combination is what's causing you problems.

First, the biggie. I'm fairly confident your cooler is on the wrong way around. 99% of air coolers with a single fan provided use this fan as a push-fan, meaning it should be at the front of the heatsink, pushing air out of the back. This image would suggest yours is no exception. Turning it around should make a substantial difference but at a glance this might not be as easy as it seems (see point two)- on the plus side it does give you the chance to check how well the cooler is seated. If you can't point it upwards then I'd try pointing it to the rear of the case, it's not ideal but it's better than you have now.

Secondly, your motherboard wasn't a great pick for the case it went into. This is always tricky at ITX, far more so than you might think, and it can have some awkward ramifications. The connectors along the top of the board potentially clip/block your exhaust fans, reducing their impact, but this is a relatively trivial issue and might only be worth a degree or two. The bigger issue is that the CPU socket location on most MSI boards is too close to the PCIe slot - compare this to the ASRock equivalent. This limits your cooler selection, might prevent you from flipping your cooler around as it's asymmetrical, and even if it does fit you have the fan nearly flush against the backplate of the graphics card, limiting it's effect.
Compare your picture with a large space up at the top and a small gap between the graphics card and CPU cooler, with this build, which has the aforementioned Arctic Freezer 13. Due to a better motherboard layout, it looks a lot more comfortable.
None of that info is helpful to your plight and I apologise, but it might put a few things in perspective and help anyone else with similar issues searching these types of thread.

Thirdly the aforementioned graphics card issue. It's a big card, and it's going to throw around a decent amount of heat. EVGA themselves will point out that any of their cards will work in the Hadron Air (more or less), so I assume they are more confident than I am, and it's possible if you can get the CPU cooling working better in itself that the graphics card will be less of a potential problem.

Onto solutions -

• 
  ■ Flip the CPU cooler, check the seating of the cooler too. If that's not possible, try it facing the rear of the case, but you might need to look at alternatives.
  
  ■ Fans. There's not a lot you can do here really, but if your fans are connected directly to your motherboard you should check in your BIOS that they are set to their maximum. It's also possible to replace the fans with higher airflow versions, but this will likely make a fairly small difference.
  
  ■ Replacing components. It's not ideal by any means, but if the setup you have right now isn't working, and isn't going to work, then this might be the best option.
  The easiest option is to get a new case with less limitations which fits everything you have already, the Fractal Design Node 304 springs to mind. Main downside is you'll need to buy a PSU too.
  The other alternative is to replace the motherboard. It's an expensive component and is arguably the most annoying thing to replace, but going for a Z87/Z97 with a better layout might make a massive difference and might even give you the headroom to overclock. If this is never going to be a priority, there's always H87/H97 options too, which will keep costs down.
  
  ■ Finally, there is modding. Google will show you various mods for this case, like the one you linked earlier, and this one. It's certainly a labour of love, and probably not the best way to get your machine up and running.

The reason I assumed you were overclocking is that the main (sole) function of a Z-series motherboard and a K-series processor is their overclocking ability. It certainly is possible to overclock in a Hadron Air, as I've seen solid results posted here before, but if you are struggling then it's obviously a no-no.