This is the only solution I have found and defeats the purpose of both Joomla and TemplateToaster. If someone with no scripting knowledge where to create a menu within Joomla that they did not want to covert to a hamburger menu not only would this not be desirable but the menu itself would be broken on mobile screen sizes.
Perhaps there is something I missed, if anyone is aware of an easier solution to this problem please let me know.
the classes I removed from the menu: "menu-center (not sure if this one is required however I removed it just to be safe)", "collapse", "navbar-collapse", "navbar-default". Here is a link for information on how to remove a CSS class via JS.