If I understand you correctly, every page but the front page is handled by WordPress, while the front page is a single static HTML file (say, index.html). In that case, if you want the Wordpress header and footer, you would be better off letting Wordpress handle the front page, too.
To heavily customize the front page, you can let the Wordpress template hierarchy work in your favor. In your theme folder, add a file front-page.php with the following content:
<?php get_header(); ?>
<!-- here is your own content, that was previously in index.html -->
<?php get_footer(); ?>