ctools.install calls drupal_install_modules(), should call module_enable()

ctools_update_6003 and ctools_update_6007 call drupal_install_modules which is not in Drupal 7, they should call module_enable which in Drupal 7 now includes the $enable_dependencies option.

/**
 * Take over for the panels_views module if it was on.
 */
function ctools_update_6003() {
  $result = db_query('SELECT status FROM {system} WHERE name = :name', array(':name' => 'panels_views'))->fetchField();
  if ($result) {
    db_delete('system')->condition('name', 'panels_views')->execute();
   drupal_install_modules(array('views_content'));
  }
}

should be

/**
 * Take over for the panels_views module if it was on.
 */
function ctools_update_6003() {
  $result = db_query('SELECT status FROM {system} WHERE name = :name', array(':name' => 'panels_views'))->fetchField();
  if ($result) {
    db_delete('system')->condition('name', 'panels_views')->execute();
   module_enable(array('views_content'), TRUE);
  }
}

and

/**
 * ctools_custom_content table was originally here, but is now moved to
 * its own module.
 */
function ctools_update_6007() {
  $ret = array();
  if (db_table_exists('ctools_custom_content')) {
    // Enable the module to make everything as seamless as possible.
    drupal_install_modules(array('ctools_custom_content'));
  }

  return $ret;
}

should be

/**
 * ctools_custom_content table was originally here, but is now moved to
 * its own module.
 */
function ctools_update_6007() {
  $ret = array();
  if (db_table_exists('ctools_custom_content')) {
    // Enable the module to make everything as seamless as possible.
module_enable(array('ctools_custom_content'), TRUE);
  }

  return $ret;
}