SUPEE-6788 variable + block setup script. 1.) Create a new module or extend a current one. 2.) Create a new install or setup script with the variables and blocks which are not whitelisted yet.

upgrade-0.1.67-0.1.68.php

<?php
/**
 * Created by PhpStorm.
 * User: a.voelkl
 * Date: 30.10.2015
 * Time: 13:21
 */
/** @var $installer Mage_Core_Model_Resource_Setup */
$installer = $this;

$installer->startSetup();

//---------------------------------------------------
// Add variables
//---------------------------------------------------

$installer->getConnection()->insertMultiple(
    $installer->getTable('admin/permission_variable'),
    array(
        array('variable_name' => 'your/variable/name', 'is_allowed' => 1),
        array('variable_name' => 'another/modules/configvariable', 'is_allowed' => 1),
    )
);

//---------------------------------------------------
// Add blocks
//---------------------------------------------------

$installer->getConnection()->insertMultiple(
    $installer->getTable('admin/permission_block'),
    array(
        array('block_name' => 'mymodule/myblock', 'is_allowed' => 1),
        array('block_name' => 'anothermodule/blockname', 'is_allowed' => 1),
    )
);

$installer->endSetup();