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I'm supposed to add the <script... JAVASCRIPT </script>... immediately before the </body> tag. That's what google analytics tells me. Where would I add that and how? is it possible?
Your index file doesn't appear to have any markup in it at all which complicates things a bit. Two things come to mind. I'm not sure how successful either of these will be for you. You could use try to using output buffering (php.net/ob_start) and just shove your script tag inline before your header redirect, or try to stick the script tag in both of your rotating files.
Find the part of your app that displays the footer portion of your markup (wherever the closing body tag is) and include the analytics code there.
If there is more than one file that contains your footer markup then you may want to consider consolidating your markup into single files containing the unchanging portions.