I'm afraid I don't entirely follow this. However I've not had much success attempting to upgrade an existing project 'in place' (because of MVC issues rather than NakedObjects).
To migrate I would suggest you
1. Create a new MVC4 project.
2. Add NakedObjects.MVC 5 package - this should all compile without any changes.
3. Copy across any custom views/controllers and initialization code from RunWeb.