PostgreSQL – How to Edit postgresql.conf with pgAdmin 3

You need to enter the password of the database user, not the OS user. The "root password" is not applicable. Do you know the password of the database user postgres?

Most systems are set up allowing peer authentication for local connections, meaning a system user can log into the database with a database user of the same name without password. localhost is not a local connection. Its privileges are determined by host entries in your pg_hba.conf file.

Since you seem to be running Postgres and pgAdmin on the same server, I suggest you try a local connection without password. Quoting the pgAdmin manual:

On Unix based systems, the address field may be left blank to use the default PostgreSQL Unix Domain Socket on the local machine, or be set to an alternate path containing a PostgreSQL socket.

Bold emphasis mine.
Of course, you have to run pgAdmin as the system user postgres for this to work.

This related answer on SO has a lot more details and links.

But that is 9.1. - Is pgadmin connected to the wrong postgresql?

Yes.

It appears that you're connected to your 9.1 server, suggesting that 9.1 is still running.

Do pg_lsclusters to see what PostgreSQL installs you have and their status.

Each runs on a different port. If you want to connect to 9.3 you need to check what port it runs on and connect PgAdmin to that port.