Restarting Amazon EMR cluster

I'm using Amazon EMR (Hadoop2 / AMI version:3.3.1) and I would like to change the default configuration (for example replication factor). In order for the change to take effect I need to restart the cluster and that's where my problems start.

How to do it? The script I found at ./.versions/2.4.0/sbin/stop-dfs.sh doesn't work. The slaves file ./.versions/2.4.0/etc/hadoop/slaves is empty anyway. There are some scripts in init.d:

$ ls -l /etc/init.d/hadoop-* -rwxr-xr-x 1 root root 477 Nov 8 02:19 /etc/init.d/hadoop-datanode -rwxr-xr-x 1 root root 788 Nov 8 02:19 /etc/init.d/hadoop-httpfs -rwxr-xr-x 1 root root 481 Nov 8 02:19 /etc/init.d/hadoop-jobtracker -rwxr-xr-x 1 root root 477 Nov 8 02:19 /etc/init.d/hadoop-namenode -rwxr-xr-x 1 root root 1632 Oct 27 21:12 /etc/init.d/hadoop-state-pusher-control -rwxr-xr-x 1 root root 484 Nov 8 02:19 /etc/init.d/hadoop-tasktracker

but if I for example stop the namenode something will start it again immediately. I looked for documentation and Amazon provides a 600 pages user guide but it's more how to use the cluster and not that much about maintenance.