creating a backup of a web server

Process followed for creating a copy of one of our web servers on a backup server - 

• Copied the conf files using sftp.
• Created the user using adduser 
• mkdir downloads as the new user,
• added to www-data group and changed permissions as on our server,
  # chown nameofuser:www-data downloads
  # chmod 755 downloads
  
  
• Check if server2 has enough disk space before running rsync.
  Currently seems to have ~600 GB available.
  
  
• Ran a2ensite for all the missing sites, and 
• service apache2 reload
  

Edit: Now that the servers run https sites, must remember to set up suitable ACME clients as available for the respective OS, for managing LetsEncrypt certificates. 

For up-to-date Ubuntu-based Linux distros, 
sudo apt install certbot python3-certbot-apache

For older distros without support, acme.sh is what I have used in the past.

For Windows, win-acme is a good option.