Right is reordered in which sense?
The right sidebar stays under the content 'cause is placed after the content from the start.
And sorry you say "the script is now in the header" you meant in the footer right?
Well the thing is that, don't know what you did, but there's something not working there.
Look what should be in your page :
<script type='text/javascript'>
/* <![CDATA[ */
var TCParams = {"FancyBoxState":"1","FancyBoxAutoscale":"1","SliderName":"fds","SliderDelay":"5000","SliderHover":"1","SmoothScroll":"linear","ReorderBlocks":"1","HasComments":"","LeftSidebarClass":".span3.left.tc-sidebar","RightSidebarClass":".span3.right.tc-sidebar"};
/* ]]> */
</script>And clearly is not there. Those lines are for passing params to scripts. Customizr uses this technique to pass params such as "Reorder Blocks" to tc-scripts.js . You can see where here:
customizr/inc/class-fire-resources.php line 124 (in customizr v3.1.10)
http://codex.wordpress.org/Function_Reference/wp_localize_script