My computer is suddenly slow but I’ve scanned for malware and viruses and there isn’t anything. Is something lurking in the background?
Please follow this guide and attach logs (Malwarebytes, OTL, ADWCleaner and aswMBR).
When done malware removers will help you from there. 
When I run otl it says:
Cannot create file C:\Users********\Downloads\cmd.bat
******** is instead of my name
Thats weird.
Try to attach the other logs when you can run these programs.
Maybe a malware expert knows more about your problem.
Logs.
A malware expert will help you soon.
Maybe he knows whats going on with OTL.
Could you move OTL to the desktop and try again please
Yep, done. OTL log.
No apparent malware so we may be looking at a driver conflict. Let me know if the clean boot option alleviates the problem
Step 1: Start MSConfig
Click Start, type msconfig in the Start Search box, and then press ENTER.
If you are prompted for an administrator password or for a confirmation, type the password, or provide confirmation.
Step 2: Configure Selective Startup options
1.In the System Configuration Utility dialog box, click Selective Startup on the General tab.
https://dl.dropbox.com/u/73555776/Cleanboot1.JPG
2.Click to clear the Load Startup Items check box.
Note The Use Original Boot.ini check box is unavailable.
3.Click the Services tab.
https://dl.dropbox.com/u/73555776/cleanboot2.JPG
4.Click to select the Hide All Microsoft Services check box.
5.Click Disable All, and then click OK.
6. When you are prompted, click Restart.
When I do that the computer just freezes and I have to manually turn it off.
OK lets now run a disc check
Step by step guide here http://www.w7forums.com/threads/how-to-use-chkdsk-check-disk.448/
Slowing down can also be caused by a heat problem.
Have you opened the system and removed all dust from hd’s, heatsinks, fans etc. ?
To remove the dust from a psu, you will have to take it out and open it.
Disk returns no errors. Fragmentation was 21% so I’ve tried with that and reduced it to 8%.
Speedfan says HD0 is 30C
Core 0 is between 49C and 50C.
Core 1 is between 46C and 49C.
Temps look OK but defragmentation was high and still is at 8%
Has there been any improvement ?
Sounds like it is time for some hardware checks.
http://www.memtest.org/
Let it do 10 passes or more. (overnight)
Sometimes a problem with the memory doesn’t appear at each pass.