Thanks guys, I did run the Windows Defender. It did find some things but they were items that i have had for a long time that always get flagged for various reasons. I did quarantine them. I'm still getting a clean reading from MSE, Malwarebytes,Ad-aware when doing the quick scan. The full scans are still leaving me with a frozen comp when i wake up after letting it run over night.
As for the HDD, I have heard odd noises coming from the box and assumed it was the HDD but was not sure. If I replace the HDD I would like to upgrade to a Solid state drive. Any idea what minimum size i need to run Win7 (64)? I have 2 HDD's now and run OS on one and the files are saved on another. How do i know which one is the problem?
The Case fan issue i believe could be from the fact that I have a Corsair external CPU fan mounted to the outside of the box and it covers half of the box fan. I keep the box access panel off to help with the cooling. I also have a 6" wall fan that i have blowing directly onto the HDD's.