vicwooten Hello
Apologize for this late response, somehow I missed your topic. Below are my answers for your questions:
This template is quite clean and the side menu there inherits layout + settings from the default menu module of Joomla. In the new version of Joomla, the layout of this menu module has been changed so it caused that issue.
I just overrode this menu module in template for you: /templates/shape5_vertex/html/mod_menu/default.php
and customize style: /templates/shape5_vertex/css/custom.css
This menu module looks the same with old one now.