Hello!
Thanks for sharing Your secrets with us.You did magnificent job on this image.There is special program ,which do it for You,it is called Helicon Focus and You cab find detailed review about it here
http://luminous-landscape.com/tutorials/Helicon.shtml
Greetings.........................Wojtek
PS.You are right about differences in images.You will need a slide to make it correct or above software(pretty expansive)