Maybe it's time to start using nginx if you want to use websockets. It's possible to setup it on Apache, but there are some drawbacks of such approach.
As for log file. Most probably Passenger tries to store the records at /var/log/apache2/error.log
As for port for Node.js app. In case of Passenger it doesn't make sense. It completely virtual (you declare any port in your app), because Passenger acts as app server, catches the requests and serves the app.