Help Removing JS/Downloader.Agent

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I have a few html files on a secondary harddrive. They wound up getting infected with JS/Downloader.Agent. This came to my attention when my AVG-free was scanning my computer. I immediately moved them to the virus vault after the infamous "Error while handling *.htm" came up. I have a HJT log, but I will attach it later in case you don't need it. I have attempted the SmitFraudFix.exe utility in safe mode to no avail. Hopefully that didn't cause any more damage. These files are important to me as they are the foundations for my uncle's website. Any help would be greatly appreciated. Thanks so much!
 
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