See below for recommendations. Let me know if you'd like any advice or to discuss this.
It would be really helpful if the README.md described the plugins used, how they're used and where they were obtained from (including licensing information etc.). We definitely need to ensure everything is properly licensed.
I think the JavaScript file organisation would be helped by more clearly separating the files into their respective responsibilities and naming them accordingly.
It's not clear from the current organisation what is third-party code and what has been written in-house. The creation of a 'lib' directory for third-party code would make this clear. As a more general observation, using something like 'Bower' would make this dependency management much clearer.
In addition to the suggestion above I'd suggest making a clear delineation between function declaration and invocation (typically in response to handlers). For the old tna JavaScript I'd approached this by having a 'tna-definitions.js', a 'tna-bindings.js' file and a 'tna-run-on-page-load.js' file.
The code seems to be using a third-party Cookie plugin but also contains code written to fix an issue with the plugin being able to get cookies. I'd suggest either finding out what the issue is with the plugin and using it or dropping the plugin altogether.
The JavaScript for this application is quite complex and would benefit from some tests. I'm not suggesting we write tests for everything at this stage but it might be worth looking at testing those key parts of the application.
See below for recommendations. Let me know if you'd like any advice or to discuss this.