Migration script example for custom Joomla migrations, related article: http://magazine.joomla.org/issues/issue-mar-2014/item/1794-complex-joomla-15-migration-with-minimal-downtime

migrate.php

<?php
define('_JEXEC', 1);

// Connect with Joomla
define('JPATH_BASE', __DIR__);
require_once JPATH_BASE . '/includes/defines.php';
require_once JPATH_BASE . '/includes/framework.php';

// Database connection
$db = JFactory::getDBO();

/**
 * Module changes
 */
 
// Get the modules that need changes
$query = $db->getQuery(true);
$query->select('*')
	->from('#__modules')
	->where('id IN (233,294,357)');
$db->setQuery($query);
$modules = $db->loadObjectList('id');

foreach($modules as $module)
{
	$module->params = json_decode($module->params);
}

// Change startLevel
if ($modules[233]->params->startLevel == 2)
{
	$modules[233]->params->startLevel = 3;
	echo('<strong>Module [233]:</strong> startLevel: 3 <br/>');
}

// Set menutype
if (empty($modules[294]->params->menutype))
{
	$modules[294]->params->menutype = 'mainmenu';
	echo('<strong>Module [294]:</strong> menutype: mainmenu <br/>');
}

// Hide breadcrumb "You are here"
if (!$modules[357]->params->showHere)
{
	$modules[357]->params->showHere = 0;
	echo('<strong>Module [357]:</strong> showHere: 0 <br/>');
}

// Save new module params
foreach($modules as $id=>$module) 
{
	$params 		= json_encode($module->params);
	$mod 			= new JObject();
	$mod->id 		= $id;
	$mod->params	= $params;
	
	$result = $db->updateObject('#__modules', $mod, 'id');
}

/**
 * Component changes
 */
 
// ZOO access fixes
$query 		= $db->getQuery(true);
$fields 	= array('access=1');
$conditions = array('access=0');
$query->update($db->quoteName('#__zoo_item'))->set($fields)->where($conditions);
$db->setQuery($query);

$result = $db->query();
echo('<strong>ZOO:</strong> Access set to 1 <br/>');