The super-cache plugin leaves a comment in the feed but that is not the problem. The <script> section of the Beacon Ad makes the feed not valid.
I would search in all the files of the blog for this comment and the <script> section e.g. with Scite.
If it is not in the files then it is maybe in some old and unused option in the wp_options database table. If you uninstall a plugin then sometimes the plugins don't remove options database entries on removal. Maybe there something left over of the super cache plugin. (You could search the super-cache plugin files for strings like get_option('name_of_the_option') to find out the names of the options of the plugin.)
On the other hand if you have made changes to the WP core files and you do not remember which files you had modified and you want to remove the changes then you could remove all core files and upload fresh WP files.
If after such an action these lines after the end of the RSS Feed are appearing then it is maybe in one of the theme files (e.g. functions.php).
I have no idea how these snippets ending up after </rss>. But it seems to me that the comment of the super cache plugin and the JS snippet of Beacon Ad are placed there with the same method.
If both are hard coded to a file e.g. /wp-includes/feed-rss2.php then you will maybe find both when you are searching for one of them.
But it is likely that these lines of codes are added dynamically by some function in one of the files. Because they are in every feed.
One possibility to add something after the </rss> tag is to use the action hook e.g. do_feed_atom -> add_action('do_feed_atom', 'add_something_after_the_end_of_the_atom_feed');
The function would look somehow like:
function add_something_after_the_end_of_the_atom_feed() {
echo "\n <!-- Hello World --> \n";
}
This could be in a theme or a plugin file (or a modified WP core file).
Either way your best chance to find these lines, is to search on the PHP files of your blog for the lines which you can see in the source code of the news feeds.
So download all the files of your blog e.g. via FTP and use a program like Scite to search.