Don't know exactly where you're coming from but you have probably started in the right place.
Here are a couple of thoughts. Firstly have a good clean out with CCleaner link text
Then run your Chkdsk /r but expect it to take between 8 and 24 hours, depending on the size of the Hard Drive.
Thirdly you can try Defrag again, but remember to turn off all software, including Screen-savers and Automated Search Engines, if this has not been done for a while, 4 to 8 hours is the period you should allocate for this.
Malwarebytes should be in there somewhere link text as well as running an up-to-date AntiVirus.
Finally, install SP3 asap!