Javascript/CSS from module not loading
Based on your edit including html.tpl.php, I agree with Chapa that's it very, umm, "Un-Drupaly".  This is the default system rendering of html.tpl.php:

&lt;!DOCTYPE html PUBLIC "-//W3C//DTD XHTML+RDFa 1.0//EN"
  "http://www.w3.org/MarkUp/DTD/xhtml-rdfa-1.dtd"&gt;
&lt;html xmlns="http://www.w3.org/1999/xhtml" xml:lang="&lt;?php print $language-&gt;language; ?&gt;" version="XHTML+RDFa 1.0" dir="&lt;?php print $language-&gt;dir; ?&gt;"&lt;?php print $rdf_namespaces; ?&gt;&gt;

&lt;head profile="&lt;?php print $grddl_profile; ?&gt;"&gt;
  &lt;?php print $head; ?&gt;
  &lt;title&gt;&lt;?php print $head_title; ?&gt;&lt;/title&gt;
  &lt;?php print $styles; ?&gt;
  &lt;?php print $scripts; ?&gt;
&lt;/head&gt;
&lt;body class="&lt;?php print $classes; ?&gt;" &lt;?php print $attributes;?&gt;&gt;
  &lt;div id="skip-link"&gt;
    &lt;a href="#main-content" class="element-invisible element-focusable"&gt;&lt;?php print t('Skip to main content'); ?&gt;&lt;/a&gt;
  &lt;/div&gt;
  &lt;?php print $page_top; ?&gt;
  &lt;?php print $page; ?&gt;
  &lt;?php print $page_bottom; ?&gt;
&lt;/body&gt;
&lt;/html&gt;


You see where it says:

&lt;?php print $styles; ?&gt;
&lt;?php print $scripts; ?&gt;


That's where Drupal dumps your JavaScript and CSS files.  If you're not making those calls chances are you're not going to get any included files.  I guess to verify this you'd also have to edit in your header.php and footer.php files so we can see what they contain.  This is where you want to start looking.

I recommend backing up your existing html.tpl.php file to somewhere, and then overwriting it with the system version of it, which can be found at modules/system/html.tpl.php relative to the root directory of your site on your system.