I think you will need to run most of it again. And then some. This is what I would have done. I assume you run XP Home:
1. Run CCleaner and reboot. The last download link on this page:
http://www.ccleaner.com/download/builds2. Run the free Malwarebytes' Anti-Malware quick scan. Link:
http://www.malwarebytes.org/mbam.php3. Run chkdsk again. Copy and paste this into "Run": CHKDSK C: /f/r
4. Run scannow. Copy and paste this into "Run": sfc /scannow. Reboot when the little progress bar disappears.
5. Run the free Windows Live OneCare online scanner. Full scan. (Note that there's a special link for Vista users.) Link:
http://onecare.live.com/site/en-us/default.htm?mkt=en-us. Reboot.
6. Visit Microsoft Update. Make sure to click the Custom button. NOT Express. Install whatever updates recommended
7. Install and run Secunia PSI - remember to activate Advanced. Install recommended updates. Reboot. Link:
http://secunia.com/vulnerability_scanning/personal/8. Open Defraggler -> Help -> About. Check that you have the latest version 1.14.159. Update Defraggler if not. Link:
http://www.piriform.com/defraggler9. Defrag freespace. Open Defraggler -> Action -> Advanced -> Defrag Freespace
10. Run Defraggler's analyze and post back here. Tell us the result.
I know this is a lot. But all systems need a "spring cleaning" at least twice a year anyway.