Well, in my case I had the same issue(request).
I started from modifying the homepage, as I added some custom layout there related to our company (dashboards, quick access to other plugins and so on).
After that I’ve created custom plugins and added all my custom layout/functions there.
Menu and header remained actually the same, but from menu I deleted all the content types so now I have there only my plugins.
Also to display layouts based on roles you should upgrade your strapi license to get custom roles. That way you create custom roles and then in the custom plugins you can verify what permissions user has and display things conditionally.