Where to add the permalink in this function?

Make use of the get_comment_link function in your foreach loop like so:

foreach ($comments as $comment) { 
    $output .= '<li><strong>'
            . $comment->comment_author
            . ' said</strong> : "'
            . '<a href="'
            . get_comment_link( $comment->comment_post_ID )
            . '">'
            . strip_tags($comment->com_excerpt)
            . '..."</a></li>';
}