Drupal 7 html.tpl.php vs page.tpl.php variables questions/thoughts
Something to keep in mind is that Drupal doesn't work with templates the way a traditional MVC framework will. Ideally you want to have as few templates as possible in your theme, i.e having only one page.tpl.php with some conditionals would be best. If you do need to split things up you can define additional templates with hook_theme() in your theme's template.php and move your header/footer section into there, but in general you'll have better results by not having lots of template variations.