First. Run Ccleaner to fix all errors you might have caused. Then start from there. Defrag after that.
Its not helping the External Drive problem, but it did clean up most of my registry errors. I haven't defraged it yet, but I'm starting to worry now because when I open my External Drive in my pc, most of the folders that was inside were gone! They weren't really deleted, they're just sorta hidden that i had to redirect them via Address bar or my bittorrent. I keep having problems with file location and saving when i open the External Section.
When I downloaded the CCleaner i also downloaded an AVG antivirus as well (I didnt have any antivirus on but I installed one just in case). Viruses were found and taken care of (a couple of trojans were found, but AVG said he dealt with it) and still nothing. Im waiting for a solution here until this thing is resolved.