@dmitri82 I copied all the scripts off my layout.tpl and added them to the core_htmlheader.tpl and got rid of the matching jquery/1.4.2/jquery.min.js that I had so there was only one. Then I placed the
<?php
Template::Show('core_htmlhead.php')
?>
at the bottom where the scripts were. I kept my Boostrap scripts up top as those dont mess with anything. I hope this makes sense.