You should not edit the files in the lib folder unless nothing else is possible. The files in the lib folder often get updated and will overwrite your changes.
The config object in lib/setup/config.js are the defaults, you can set all of them in app/config/config.json. The default for the port is getting it from the PORT environment variable or 3000 if that is not set. The settings in the config.json will overrule it.