404 permalink errors on Pages only

can you try replace

RewriteRule . /cpu/index.php [L]

by

RewriteRule . /index.php [L]

as for a way to debug…

well you can always var_dump a $wp_query object to get an idea what variables not passed to wp. (you can place ) into first line of your header.php template.

and i belive next step will be debug of rewrites in this case usefull filter is rewrites_array_rules which you can use for debug proposes in a next way

add_filter('rewrite_rules_array', 'rewrite_rules_array_filter_debug', 10000);
    function rewrite_rules_array_filter_debug($rules){
    var_dump($rules);
    return $rules;
}

add this to header php

   <?php 
          global $wp;
          echo '<pre>';
          var_dump($wp);
          echo '</pre>';
   ?>

this shoudl give you a point what rewrite rulle trigger to you page request.