>> Have I completely misunderstood what I need to do in order to set this up?
Hi. Nah, I think that the header.php and footer.php files need to have access to the header-footer class/script so that echo $Navigation->getHeader(); and echo $Navigation->getFooter(); output the header and footer.
Perhaps add an include("/path/to/class/script.php"); into header.php and footer.php, and then call just header.php and footer.php from the browser to check and see if the HTML is onscreen.
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