Hook form alter to filter reference CT in onother CT

custom.module

/**
 * Hook form_alter
 */
function custom_form_alter(&$form, &$form_state, $form_id) {
  switch ($form_id) {

    // alter the dropdown for the products, used by a success story
    case 'success_stories_node_form':

      $language_map = array(
        'nl' => array(
          'node/59',
          'node/60',
          'node/97',
        ),
        'fr' => array(
          'node/184',
          'node/185',
          'node/186',
        ),
        'en' => array(
          'node/115',
          'node/154',
          'node/155',
        ),
      );

      $rtn = array();

      foreach ($language_map as $language_code => $paths) {

        $rtn[$language_code] = array();
        $tmp = array();
        foreach ($paths as $path) {
          if ($children = _custom_get_menu_children($path)) {

            _custom_refactor_children($tmp, $children);
          }
        }

        $rtn[$language_code] = $tmp;
      }

      $form['field_related_product'][LANGUAGE_NONE]['#options'] = $rtn;

      break;
  }
}

/**
 * Refactor the menu children for display in the select list
 * 
 * @param Array $tmp
 *   the target array
 * @param Array $children
 *   the menu children
 * @param int $lvl
 *   what level you are refactoring
 */
function _custom_refactor_children(&$tmp, $children, $lvl = 0) {
  foreach ($children as $nid => $child) {

    $prefix = str_repeat("--", $lvl);

    $tmp[$nid] = $prefix . $child['title'];
    _custom_refactor_children($tmp, $child['children'], $lvl + 1);
  }
}

/**
 * Check if the parent can be found and return the children
 * 
 * @param String $path
 * @return
 *   the chidlren 
 *   FALSE on failure
 */
function _custom_get_menu_children($path) {
  $plid = db_query("SELECT mlid FROM menu_links WHERE link_path=:path", array(
    ':path' => $path,
      ))->fetchField();

  if ($plid)
    return _custom_get_menu_children_from_plid($plid);
  else
    return FALSE;
}

/**
 * Get a full list of children
 * 
 * @param int $plid
 * @return Array
 *   the children keyed by nid
 *    values: title, children
 */
function _custom_get_menu_children_from_plid($plid) {
  $mlids = db_query("SELECT mlid FROM menu_links WHERE plid=:plid", array(
    ':plid' => $plid,
      ))->fetchCol();

  foreach (array_values($mlids) as $mlid) {
    $nid = db_query("SELECT link_path FROM menu_links WHERE mlid=:mlid", array(
      ':mlid' => $mlid,
        ))->fetchField();

    if (!$nid)
      break;

    $nid = str_replace("node/", "", $nid);

    if (is_numeric($nid)) {
      $rtn[$nid] = array(
        'title' => db_query("SELECT title FROM node WHERE nid=:nid", array(
          ':nid' => $nid,
        ))->fetchField(),
        'children' => _custom_get_menu_children_from_plid($mlid)
      );
    }
  }

  return $rtn;
}

function custom_submenu_tree_all_data($path, $menu = 'main-menu', $curr_level = 0, $rebuilt_path = '', $childtree = array()) {

  $tree = menu_tree_all_data($menu);
  $args = explode('/', $path);

  $rebuilt_path = empty($rebuilt_path) ? $args[$curr_level] : $rebuilt_path . '/' . $args[$curr_level];

  foreach ($tree as $branch) {
    if ($branch['link']['link_path'] == $rebuilt_path) {
      $childtree = $branch['below'];
      if ($rebuilt_path != $path) {
        $curr_level++;
        MY_MODULE_submenu_tree_all_data($path, $menu, $curr_level, $rebuilt_path, $childtree);
      }
    }
  }

  $items = array();
  foreach ($childtree as $child) {
    $items[] = l($child['link']['title'], $child['link']['link_path']);
  }

  return theme('item_list', array('items' => $items, 'attributes' => array(), 'type' => 'ul'));
}