Upgrade from 2.2.1 to 3.1.2: Breaks JS and CSS?

Upgraded from 2.2.1 to 3.1.2. The upgrade went fine but most JS and CSS seems to be broken.
Examples
1. Javascript functions not defined: redirect, html_ShowElement
2. Template button images are broken. See http://i41.tinypic.com/294pgso.jpg
My page templates are mostly unchanged, i.e. they have stuff like
#HEAD#
<title>#TITLE#</title>
<link rel="stylesheet" href="#IMAGE_PREFIX#themes/theme_10/theme_V2.css" type="text/css" />
This seems to be generating the following HTML
<script src="/i/javascript/htmldb_html_elements.js" type="text/javascript"></script>
<script src="/i/javascript/htmldb_get.js" type="text/javascript"></script>
< link rel="stylesheet" href="/i/css/core_V22.css" type="text/css" />
< ! -- [ if IE]><link rel="stylesheet" href="/i/css/core_ie_V22.css" type="text/css" /><![endif]-->
< link rel="stylesheet" href="/i/themes/theme_10/theme_V2.css" type="text/css" />
Version 3.1.2 seems to have changed stuff around. I tried creating symbolic links from htmldb_html_elements.js -> apex_3_1.js and htmldb_get.js -> apex_get_3_1.js and this got me past the Undefined errors but now I get 'apex is not defined'.
Is there a quick way to upgrade all the applications to the new way of doing things? I am not looking forward to modifying all my page templates!
Help!
Thanks

Sorry, my fault, my database got refreshed from one containing Apex v 2.2.1 without my knowledge and the OHS images folder was still pointing to the that from the 3.1.2 distribution. This was causing the problem. When I upgraded Apex to v3.1.2 again, everything is back to normal.
The #HEAD# substitution string in my page templates automatically pulls in the appropriate JS/CSS libraries
<script src="/i/javascript/apex_ns_3_1.js" type="text/javascript"></script>
<script src="/i/javascript/apex_3_1.js" type="text/javascript"></script>
<script src="/i/javascript/apex_get_3_1.js" type="text/javascript"></script>
<script src="/i/javascript/apex_builder.js" type="text/javascript"></script>
<link rel="stylesheet" href="/i/css/apex_3_1.css" type="text/css" />
< ! -- [ if IE ]><link rel="stylesheet" href="/i/css/apex_ie_3_1.css" type="text/css" /><![endif]-->
<link rel="stylesheet" href="/i/themes/theme_10/theme_V2.css" type="text/css" />
Sorry for the false alarm
Thanks

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