PC turning off after about 2-3 minutes

The heat sink is a older version of this
http://www.asetek.com/desktop/cpu-coolers/545lc.html

Those squares are power phases and they usually do get pretty hot.

1) You are using to much or to little thermal paste

2) You aren't attaching the heatsink right

3) Your voltages are to high

I put a little dot on it and spread it evenly. The entire processor was covered with a thin layer. Couldn't see through it, it was kind of a dark grey paste.
I didn't change anything on my pc since I got it so I don't know how it could be the voltages.

Also, the heatsink has slits on the sides of it that attach to this metal piece that screws into the mother board so it is attached correctly.

Without seeing it, it is hard to know if you used to much/to little or the right amount. You only need small dot about the 5-5.5 mm's in size or about the size of a pea. I also wouldn't spread it I as that can cause air bubbles that can cause heat problems. Also two more things have you checked to make sure the fan is fully working and have you gone into the BIOS to make sure the fan in spinning at the right RPM?

One more thing down load CPUID HwMonitor and monitor the temps. That way we can know that it is overheating that is causing the problem and not something else like a PSU or other hardware.