Have a look at this excellent question and answers on Server Fault that discusses how to secure your LAMP stack.
Make sure your FTP user can only access the directories you want.
Setup sudo to allow a non root user to run commands as root.
Lock down your ssh so that root cannot log in set
PermitRootLogin = no in /etc/ssh/sshd_config
Enable passwordless public key login for ssh.
Disable ssh password login
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