Hi! I thought that html has a special place for the .js file. See here:
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Source code
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<script src="tour.js"></script>
<div id="pano" style="width:100%;height:100%;">
<noscript><table style="width:100%;height:100%;"><tr style="valign:middle;"><td><div style="text-align:center;">ERROR:<br/><br/>Javascript not activated<br/><br/></div></td></tr></table></noscript>
<script>
embedpano({swf:"tour.swf", xml:"tour.xml", target:"pano", html5:"auto", passQueryParameters:true});
</script>
</div>
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Maybe, place your .js where it should be (see where 'tour.js' is in the above example) and not try to hammer it in the place of .xml?
I've never tried embedding xmls into .js, however, so this is a guess only...