Straight 5200 does not have a cooling fan, it has a medium profile heat sink. Cannot be the problem.
Check the CPU cooler, sometimes they get a little out of alignment when components get replaced. The preffered way would be to remove the cooling system, clean the contact pad, reapply a little thermal compound to the contcat point and reinstall. Also, check your case fans, and if you have a side mount check it, as they have a tendency to get torqued.
HDD make a very distinct sound, it's a metalic, scratching, sand in your disc brakes, electro-mechanical screech. There are many S.M.A.R.T. HDD readers out there, use a free one, and read the status. Here is one:
http://download.com.com/3000-2086-10...ml?tag=lst-0-1
This taps into the HDD self diagnostic report system, and "should" produce a user readable explanation of the system diagnostic.
HDD are "always-on" devices, until one sets it otherwise in the power management area. Just a little advice, never set HDD to power down or go to sleep under power settings. That is adding undue stress, and taking life cycles off of device.