If you cleaned up your indenting a little to make this more readable, you would find some interesting things going on that you probably don't expect. For example, this chunk of code:

   while (( $fig, $img) = each(%images))
                        {
 
                                grep{$fig} "$html_dir/$FigFile/$DirFil
+e";
                                        s/$fig/"<a href = $img>$fig<\/
+a>"/g;

                        %images = ();
                        }
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is getting run once for every line in every file you analyze. I suspect you only wanted to run it once per file, rather than once per line, which is probably causing it to take a great deal more time than you would have expected.