Thanks for granting me access to your site. I enhanced my plugin to get around those errors caused by your infection and the Complete Scan is working again. I also expanded the Scan range to include the root of the public_html folder (this include the other sites on your server that were infected too).
I downloaded everything in your public_html directory using the FTP credentials you gave me and then ran the Automatic Repair. It clean all the infected files, even in the directories that had errors previously.
You should be ready to request a review in Google Webmaster Tools to clear that warning on the search engine results.
Please let me know if you need any more help. Otherwise you can mark this topic "Resolved".