I have the Intel's Stock cooler installed. And the PC is 2 yeas old. I only have a Back panel fan installed.
And another thing is that whenever i turn on my PC the CPU fans spins in high rps for about 3 secs and then become normal.
The fan speed you detect is quite normal. That is Speedstep in BIOS/CPU taking over the control of the fan's speed.
With only a single exhaust fan in your case, you are probably not getting as much air flow as you should for stressful situations (like gaming). I would blow the dust from the CPU's cooler and fan, and add a front and/or side case fan for extra cooling. If you don't O/C, the stock Intel cooler should be more than adequate as long as the case has good air flow.
If you decide to replace your TIM, MX-4 is a good choice. It is at least as good as AS-5 and has the added virtue of not being electrically conductive.