The first question is discussed here: Display of keywords in OJS 3.0.2.0 I think that it would be fairly easy to solve that problem, but I am still waiting for a response regarding the two questions I asked in the last message of that thread.
Question two, you have to edit the template that contains the navigation banner or create an own theme and add an edited navigation banner template there. In OJS3.1 they are planning to have a built-in navigation management https://github.com/pkp/pkp-lib/issues/2178
Question three about the banner, I actually am not entirely sure what you mean, but I think it depends on the theme you are using.