Javascript + Magento Guru Required!

Looking for a real javascript/magento guru! I have a muti-site Magento install, in the configurable page it generates a fair bit of inline javascript (custom coded) to show live stock status and switch up images. This all works. I'm trying to integrate cloudZoom into this, at the moment it doesn't work. I have a compiled javascript file which is loaded in the footer. I'd like to move the majority of the inline javascript into that compiled file. Any of the other inline javascript, if it's possible to move to the footer that would be ideal. I have a php file which compiles the core js file so it's not too difficult to edit that core file. This is a live site. You can see an example page here: [login to view URL] Please don't bid if you are not a very experienced javascript coder, thanks.