I prefer changing all:
<?php bloginfo('template_url'); ?> and <?php bloginfo('stylesheet_directory'); ?>
into:
<?php echo get_template_directory_uri(); ?>
For connection to default style.css I prefer to change:
<link rel="stylesheet" href="https://wordpress.stackexchange.com/questions/105303/<?php bloginfo("stylesheet_url'); ?>" type="text/css">
into:
<link rel="stylesheet" type="text/css" media="all" href="https://wordpress.stackexchange.com/questions/105303/<?php bloginfo("stylesheet_url' ); ?>" />
I found no script type is defined in any of the scripts:
<script src="https://wordpress.stackexchange.com/questions/105303/<?php echo get_template_directory_uri(); ?>/js/jquery.js" type="text/javascript"></script>
The best option of using wp_head() is using it just before the closing tag, like:
...
<?php wp_head(); ?>
</head>
And the best way to using wp_footer() is using it in footer, but just before the closing </body> tag:
...
<?php wp_footer(); ?>
</body>
And beside that,
Ian Stewart’s theme development tutorial may help you understand the very core things of WordPress themes in a very easy way.
And also, WordPress by default uses some js files, so js can conflict with those in many ways. If, then you have to find out the conflicting js manually.
And for a menu CSS, I call THIS ONE a Universal Menu CSS. 🙂