The page is constructed on the server from all the PHP bits, and the full page is sent to the browser, so I really don't think that's the issue. Are the scripts actually on your server, and if so, where are they?
it works when the full page (instead of header.php,nav.php, body.php) is loaded.
Could you elaborate on that? Is there a test page you can show us?
You still have links pointing to the demo site, which just won't work. The links to all scripts should be to scripts on your server (except perhaps the jQuery library link, which could also point to the Google version or even the version on the jQuery site ... though often these days the recommendation is just to have it on your own server.)