For future reference use php to include the header information (including the favicon) that stays consistent on each page so that you only have to edit one file instead of a large number of files.
Use <?include "header.php" ?>
on all pages where your header.php includes all the code that is common to all pages
It could be something like:
<link rel="stylesheet" href="screen.css" type="text/css" media="screen" />
<script src="../quirksmode.js"></script>
<link rel="icon" href="/favicon.ico" type="image/x-icon" />
and all the other code that needs to be included on all the pages
See more about include here: http://php.net/manual/en/function.include.php
EDIT: For now you could open all files in an editor like notepad++ and do a find and replace to replace all occurrences of with \r\n where \r\n is the newline character for windows in the extended search mode. Notepad++ has the option to do a find and replace in all open files.