Several of my sites have been hacked with a base64 php hack. From everything that I've read the best way to get rid of this is to do a clean install of all of the Joomla files and all of the templates and extensions that are used on the site. After doing this you copy a cleaned version of the main configuration.php file to the new site.
Most of my sites that were hacked use RT themes and Gantry. I can't seem to figure out how to manually install either of these or things like RokGallery without losing all of my settings. Can someone point me in the right direction? I've spent several days now trying to clean up these sites. I don't want to have to start from scratch since I have several hundred hours of work into these sites.
The easiest way to salvage your work would be to backup your database, remove extensions, install them from the beginning and restore your database at the end