Your link is very broken but I guess
http://pcpartpicker.com/p/1G71M/by_merchant/ is the thing in question. First why do you have a 5900RPM hard drive in what looks to be aiming at a performance machine? You can get an entry level, but otherwise very nice, SSD for the money. About the only use these days for a 5900rpm drive in a performance system is if I need to copy something onto from a dying system -- I would not use it as scratch space, I would not use it as normal storage and certainly would not store games, the OS or something similar on it.
Anyway the cooler
http://www.amazon.co.uk/Cooler-Master-Hyper-212-120mm/dp/B0068OI7T8 says 13 x 10 x 18 cm
Your case says "Dimensions (L x W x D) 19.10" x 8.00" x 16.80""
That is just over 20cm so I anticipate a very tight fit and I could see it not fitting.
How to apply paste, clean the surface of the chip and the heatsink (something that will not leave a residue and with an item that will not do that either, put a blob on the size of a couple of grains of rice and smooth it over with a razor blade. Put the heatsink on and attach it however it says to attach it (if it offers no advice then do one screw/clip and then do the diagonal of it, then finish). The heatsink may come with pre applied paste that you can remove or you can use.
By all means overclock your graphics card as you can get a bit out of there. Why overclock a new CPU in 2013? I had a quick look and yeah it produces some boosts you might even be able to tell apart at the higher ends but nothing close to overclocking back when or even back on the likes of core2 machines. As you asked though
http://www.overclock.net/t/1348623/amd-bulldozer-and-piledriver-overclocking-guide-asus-motherboard# does not appear to suggest anything too outrageous or ignore too much science/good sense. Personally if I am going to overclock I like to leave the speedstep stuff on when all is said and done which appears to be something the OC set are loathe to do.
I already took old paste stuff. Still a cloth and some form of solvent that will not leave a residue (pure acetone like some nail polish remover works well enough) and evaporate readily. I tend to have an interesting chemical stockpile anyway so I am not sure what advice I can really offer here.
RAM. Varies depending upon when you are doing it as motherboard design changes a tiny bit.
Generally you have four concerns.
Ram frequency
Ram timings
Voltages
How they relate to the rest of the system.
Ram is rated to run at a given frequency (or less than that). The site reckons that speed in this case is 12800 Hz in this case.
Timings are largely pointless but to cover them anyway though I said 12800 it does not mean one operation (read, write, read after a write) per cycle and some chips can do more for the same amount of cycles. At least in theory, in practice it is fairly pointless as far as most tests have ever demonstrated. Where they might come up is if you want to increase the speed but drop the timings to allow for slightly more speed.
Voltages. It will be rated to run at a given voltage, you can increase this at the cost of increased amounts of heat needing dissipation and probably a lessened lifetime. However this helps with stability if you want to overclock it a bit. Likewise you could always try backing off a bit for some types of overclocking if the RAM voltage is messing with your CPU voltage, at this point though I would say call it a day and put it back to the last stable configuration, either way though that brings us nicely onto the "how it relates back" thing
How it relates gets odd. Back in the day the speed you ran your frontside bus at determined in part how fast your CPU ran (the other part being the multiplier) and also the RAM with it. Not sure when but in consumer world around the core2 era we got unlinked options which meant you could run the RAM at one clock and the CPU at another at some theoretical potential loss for not being quite synced but you could then push one or the other as far as you liked and be left with a stable system, today it seems unlinked is not quite the order of the day but you can still raise different ones at different levels.
I can not say I have really dealt with modern AMD stock coolers, such things are usually an exercise in "get it to work well enough for the consumers and no more" though I am happy enough to use them which is more than can be said for a lot of older ones. Quieter depends upon several things including the frequency it runs at (some people are more sensitive, or at least claim they are more sensitive, to higher pitched noises, some people want to hear a gnat fart when their machine is on) and how you set it up (target temperatures and whatever else). Most of the reviews reckon it is quiet though.
Better. Do you want quieter, more reliability (your chosen fan and for that matter the stock one will probably last until long after your computer has ceased to be useful unless you smoke around your PC), more cooling, more LEDs and fins to show off to cretins....? I have a great dislike of lot of consumer computer cooling companies and view a lot of what they do in the same way a chemist views shampoo commercials, skin cream commercials and much of the organic food movement. To answer the question you may be able to find a slightly quieter one or a better cooling one for similar money but I doubt there will be a "oh this is better in every way" one out there somewhere.
Anyway I am now at risk of going full grumpy old man on you all so I will stop it here.
