1) Cooler:
The NH-D14 is complete overkill IMO, and also doesn't use PWM fans. There are newer designs like the NH-U12S (I've tested this one) or NH-U14S that aren't as large but should serve you very well.
I can't hear the NH-U12S at all in normal usage and even when converting a video at 98% CPU usage (i5-4670K @ 4.2GHz) it's fairly quiet even when the ONLY fan aside from the power supply (no graphics card and turned off the case fans to test).
My advice is:
a) get the U12S or U14S,
b) set CPU/Memory in BIOS to "XMP" then save
c) test DDR3 memory with Memtest www.memtest.org
d) use Intel CPU test program (Intel site)
e) Fan control software setup for CPU/case fans as appropriate (motherboard software)
XMP will likely choose 4.1 or 4.2GHz for your CPU. It can go higher if you want but I'd start there. For one thing, in "XMP" mode you still have the Intel Power Management settings intact. If you manually overclock to say 4.6GHz you will increase the noise as some of these settings are disabled (frequency control, voltage raised etc).
I wouldn't push the CPU to the limit either. Running at 4.8GHz is far, far louder than running at 4.2GHz and it's only up to a maximum of 15% difference (probably under 10%) time savings for video conversion.
2) Graphics card:
I strongly recommend waiting for a GTX880 instead. Coming soonish and should be $500+ and have GTX780Ti performance or slightly better.
A lot of the R9-290/290X cards have issues probably due to overheating so you'd need to carefully look at customer reviews. I WANTED to recommend the R9-290 based on value but the only few I thought okay were almost the same price as a GTX780 so I ended up recommending the EVGA GTX780 967MHz card which has excellent customer feedback for quality.
3) Motherboard:
The one you chose is okay, but I think you should spend a tiny more for one with better customer feedback like the Asus Z97-A :http://pcpartpicker.com/part/asus-motherboard-z97a
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