The problem can be in the method used for cloning the sites, have you tried with the sites included in SET?
Also I have been using a tool called Nexphisher, works pretty well. Give it a try, just edit the setup script file first IT’S VERY IMPORTANT THIS STEP, so open it with leafpad and remove the line “apt-get upgrade -y”, then you can run it and it will be installed properly.
Here is the link to it:
Also you’ll find the instructions to use it there.
Let me know how it goes!