Linking back to home page in wordpress
<a href="<?php echo home_url(); ?>">Home</a>
You can use the home_url function: http://codex.wordpress.org/Function_Reference/home_url
I also recommend checking out the WordPress Function reference, and use the appropriate built in functions rather than inventing your own.
Edit: Not sure if you want to go back to the main index, or the WordPress index. If you just want to link back to your first index.php, you can simply use <a href="/>Home</a>