Here's about the simplest barebones super basic explanation I could come up with..
When writing a Wordpress website I think the first thing you should get is that where-as coding a plain HTML site you have to write the structure of the page and the content.. when you write a Wordpress page you are only writing the structure, all of the content is going to be created in the Wordpress backend user portal.
So to start, remove all the content from your code and your left with this (I'm going to remove the PHP includes and start fresh)
<!DOCTYPE>
<html>
<head>
<!-- Include stylesheet -->
<link rel="stylesheet" type="text/css" href="/style.css" />
<!-- Include scripts -->
<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js" type="text/javascript"></script>
<script type="text/javascript" src="/code.js"></script>
<!-- Page title / meta -->
<title></title>
</head>
<body>
<!-- Page container -->
<div id="wrapper">
<div id="main">
<!-- Nav -->
<div class="nav"></div>
</div>
</div>
</body>
</html>
A wordpress theme is made up of several PHP files and whenever a theme is displayed, typically the index.php file is loaded first so that's where we'll start.
Wordpress themes, most of them, amongst all the PHP files that make up the theme, there will be a header.php file, footer.php file..
So in index.php the first line we write is get_header(); (within php tags of course) This is a Wordpress function that is essentially
I assume your going to want your nav on all pages so you can cut all of this code out of your index file and paste it into header.php
<!DOCTYPE>
<html>
<head>
<!-- Include stylesheet -->
<link rel="stylesheet" type="text/css" href="/style.css" />
<!-- Include scripts -->
<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js" type="text/javascript"></script>
<script type="text/javascript" src="/code.js"></script>
<!-- Page title / meta -->
<title></title>
</head>
<body>
<!-- Page container -->
<div id="wrapper">
<div id="main">
<!-- Nav -->
<div class="nav"></div>
</div>
</div>
Back to index.php the second line we'll add is get_footer(); another Wordpress function to get footer.php.
Currently index.php would look like this now..
<?php get_header(); ?>
</body>
</html>
because everything else is in header.php.. well that closing body and html tag.. those go in footer.php. so your index.php file is going to end up looking like this
<?php get_header();
get_footer(); ?>
Header.php is going to look like this:
<!DOCTYPE>
<html <?php language_attributes(); ?>>
<head>
<!-- Page title / meta -->
<title><?php wp_title( '|', true, 'right' ); ?></title>
<?php wp_head(); ?>
</head>
<body>
<!-- Page container -->
<div id="wrapper">
<div id="main">
<!-- Nav -->
<?php wp_nav_menu(); ?>
</div>
</div>
and you know what's in footer.php. As far as those CSS and javascript files, those are going to be in your functions.php file.
Wordpress has LOTS and LOTS of prefab functions that they like for you to use and it would take forever to explain them all. Luckily a lot of that's already been done in the Wordpress Codex. Though it's got a lot to be desired as far as the quality of the documentation in some places in my opinion it is something you should spend a good amount of time reading thru before you start, in order to familiarize yourself with all their functions.