Callbacks order in Drupal 7
The code you are trying doesn't work because syntaxhighlighter_prepare_callback() and html_pre_filter_prepare_callback() are not hooks: They are simply callback functions defined in the implementation of hook_filter_info() done from those modules.

In fact, the code used by check_markup() to invoke the input format filters is the following one.

  // Get a complete list of filters, ordered properly.
  $filters = filter_list_format($format-&gt;format);
  $filter_info = filter_get_filters();

  // Give filters the chance to escape HTML-like data such as code or formulas.
  foreach ($filters as $name =&gt; $filter) {
    if ($filter-&gt;status &amp;&amp; isset($filter_info [$name]['prepare callback']) &amp;&amp; function_exists($filter_info [$name]['prepare callback'])) {
      $function = $filter_info [$name]['prepare callback'];
      $text = $function($text, $filter, $format, $langcode, $cache, $cache_id);
    }
  }

  // Perform filtering.
  foreach ($filters as $name =&gt; $filter) {
    if ($filter-&gt;status &amp;&amp; isset($filter_info [$name]['process callback']) &amp;&amp; function_exists($filter_info [$name]['process callback'])) {
      $function = $filter_info [$name]['process callback'];
      $text = $function($text, $filter, $format, $langcode, $cache, $cache_id);
    }
  }


No hook is invoked, or you would see a call to module_invoke() or similar function.

If you are looking at a way to programmatically re-order filters used by input formats, the only way I can see is altering the cache where Drupal stores the information about the input filters. See filter_list_format(), which is the function that returns an ordered list of filters used by an input format.
More easily, this can be accomplished from the user interface, since on admin/config/content/formats you order the input filter for each input format.