Computer Incredibly Slow

Don't know if this is the exact right place, if it isn't feel free to move it. 

So, I come home for Thanksgiving and my parents computer is suddenly incredibly slow. It is taking about 3-5min to boot then about another 5 for Chrome to launch. Occasionally it freezes as well. It has never been super speedy but it has never been this bad. Right clicking takes about 5-20 seconds for the menu to pop up. Opening up Explorer windows seems to take an age as well.

Thing is though, once it is up it is usually okay. Running games is fine. TF2 and JC2 are both running at 90FPS and 75 FPS on max respectively at 1600X900. Anything else though is really slow. Chrome crashes occasionally. 

I have ran antivirus and not found anything. I've removed all excessive programs and non essential startup items. Defragged the HDD. Updated drivers. Everything. Nothing I do seems to do any difference. 

I thought it might be the HDD failing, but SMART diagnostics say it is healthy and HD Tune's error check hasn't returned any anomalies either. It doesn't appear to be making any abnormal sounds either. 

I'm gonna reinstall Windows as soon as I finish backing up the HDD. I don't have a copy of Windows 7 though so is there any way I could get Windows to create an ISO for me? I did some quick Googling, and it appears possible but I've never done it before and I trust people here more than I do those on WikiHow lol

Any other ideas?

Here are the specs. It is an HP prebuilt system that I have added to:

Some MicroATX (I believe motherboard, Not sure on the chipset or anything. Gonna look in a few. SOmething like VIOLET 7 and Pegatron comes to mind IDK why) 

AMD Athlon II X4 630. 2.8Ghz Quadcore

8 GB of Kingston HyperX BLU RAM

WD Green HDD. 1TB 5400 RPM drive

EVGA GTX 650Ti SSC 1GB 

Windows 7 Home Premium 64 Bit

System is about 4 years old with 3 years on the current HD. There is no overheating as well. CPU at load is around 50 or so degrees and the GPU is at 55. low 30s and mid 20s at idle respectively

Just want to add that some flies were corrupted by a virus a year or two ago but I repaired them. However i installed TeamViewer the other day and now when I start it I get a message that a DLL file is missing or corrupted however it still runs. 

what programs are set to run at startup?  There may not be a virus, but could be malware that is not identify by an antivirus.

There are about four programs set to run at startup. They consist of the mouse software, Avast, and two others that are like software update services. I'll check in a bit. 

How does one go about removing it then?

Hm. Did you scan it with Avast, MBAM, and SpybotSD? The only thing that I believe would cause this is a virus, however; I am probably wrong.

 

Click start and in the run box type msconfig, then go to the startup tab, and there you'll see all the programs that are running at startup.   If you see anything that is running from the appdata folder, most likely is a virus.

 

I have also ran Malware Bytes. 

Only things running at start up right now are:

Hardware Diagnostics and monitoring from PC Doctor

Logitech Setpoint

Spotify 

2 instances of avast for some reason one is an updater I believe

Java Platform SE Auto Updater.

Spotify is running from the appdata folder.

Anyone know about reinstalling Windows?