How do i make a full diagnostic for software and hardware both?

Hi everyone,
because of my macbook pro(this is my first mac and only one i have) have been change logic board for three time, but i always use it nicely but still like this(maybe I overprotect it?), recently i heard "pop" sound out from the air vent, i not sure what happen or maybe it just some random sound from surrounding, i just not sure because it happen not every noticeable, so i decide to do a full scan diagnostic on hardware and software, I have months not using my mac, do i have to do a clean install, to make sure everything working, I actually having some problem in the last time i use my mac, the problem is as below:
1) the ooo sound problem as i mentioned earlier
2) iwork not update properly
3)apple hardware test not show up when press D instead internet recovery show up(only recently, before this everything fine)
4)maverick a little unstable like mountain lion
So how do i do full diagnostic an should i make a clean install instead?
Thanks for helping!!!!

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