Actually I have seen this exact this thing many times. Your database is clean and the search results you are seeing are just cached pages from January when your site was infected. My plugin fixed this infection when it cleaned the functions.php file so you just need to go to your Google Webmaster Tool and Request a Review of your site to get rid of all those cached pages that are no longer infected.
As for this folder of files that have unreadable code, can you tell me more about that? What folder is it? What are some of the file name? Can you send me a couple of those files so I can examine the contents?