Thanks for this and the last reply, (forgot to mention that in last).
My group actually handles the dev side. We're basically instructed to make specific changes. In this case the SEO/SEM PM's have instructed to add the canonical tag only on the index not on all pages. the page is index.php. And they're adamant the canonical does not reflect index specific because they don't want all pages indexed as such. I was told to use this:
<link rel="canonical" href="http://<?php echo $_SERVER["HTTP_HOST"] ?><?php echo parse_url($_SERVER['REQUEST_URI'],PHP_URL_PATH); ?>" />
I did this today. Haven't heard back from the PM's yet.