If i use header and footer separately as template for example <? require="header.php" ?> <body>content</body> <? require="footer.php" ?> obviously These will be three separate pages with different content. So there is a doubt weather this will effect adsense CPC. I think it does cause adsense CPC depends on content.
depends what's in the header/footer files. if it is just something like simple navigation links, shouldn't matter at all.
Do you expect to see google what you do on server side? Man.. they can see only HTML. Your server side logic doesnt matter. BTW, header and footer are poor places for ads. You will have to be more "on your face" to get more clicks.