Ok so I originally had jquery update installed and had it at the default 1.5 (mainly becuase I didn't know you could configure it yet).
This made navbar unusable as it broken every link on every page. I uninstalled jquery update and it fixed the problem. Site was back at the default jQuery 1.4.
This had the unintended consequence of rendering the Module List module unusable as it requires a newer version of jQuery. So as a test, I installed jQuery update again and Module List works once again. I then noticed I couldn't update the version of jQuery in jQuery Update because all my links are broken again because of navbar.
Now, I cannot even uninstall any modules to get back to a workable state and nothing works. Every link acts as though the href is "/". I can right click and open tabs in new tabs or go direct to the pages via URL, but that doesn't help since you can't right click a submit input.
So what did I do to solve the problem? Well I triggered the form on the jQuery update module config page via my console using an easy .submit(). This let me set the jQuery version at 1.8. This brought back functionality to the links, however, I'm sure there are many users out there who don't even know what a console is, let alone what to do to trigger a form submit. I'm no guru or anything, but there are people who know far less.
The state of my site is that functionality has returned, however, the overlay is not functioning with this module, nor is the inner-navbar-trays visible on the site outside of the administration pages. I.e. when using the site at example.com/ I get only the top bar (Home, Menu, Shortcuts, Site) and none of them work. They won't launch the submenu underneathe. When at example.com/admin/ I get both bars and working right. This is the next problem I'm going to tackle, but right now, any assistance is appreciated and you should note these errors for other users.