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Can you select the file with the <div id="mygallery" code as the banner file for header position 3?
You would save the stylesheet as something like stylesheet_carousel.css in /includes/templates/your_template/css/.
The js references and code should go in files named like jscript_xxx.js in /includes/templates/your_template/jscript/. I don't know the best way to organize them all, as I don't work with javascript. There are tutorials and forum threads with lots of information on the subject.