[Plugin: Magento WordPress Integration] JS load problem (wordpress end)

I have portfolio setup within wordpress that uses jquery isotope to dynamically cascade items by category. When adding this code:

<?php
// Echo full Magento head file
the_block(‘head’);

// Get specific elements from the head
$head = get_block(‘head’, false);
echo $head->getCssHtml(); // All CSS and JS files defined in your Magento head
echo $head->getChildHtml();
echo $head->getIncludes();
?>

<div id=”container”>
<?php the_block(‘header’);

?>
It loads the css and jquery from magento just fine but it stops the isotope jquery function. When removing the magento blocks from header the jquery loads. I have also tried loading js files into the magento directory and defining them within page.xml under head. let me know your thoughts. Here is some more code reference:

page.xml with added js:
https://screencast.com/t/zrUp2yXCX
header.php (wordpress with magento blocks):
https://screencast.com/t/6BOEgtqOr75w
functions.php (calls js for wordpress):
https://screencast.com/t/rkdzNKeUp
portfolio.php:
https://screencast.com/t/Bh5LnvQZn4M5

I tried be as detailed as possible, I hope this helps. Any direction at the least would be great! Thanks again, this product has allowed great things to happen.

https://www.ads-software.com/extend/plugins/magento-wordpress-integration/