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If you copied infected files from one website into the directory structure to another site then you may have copied the source of the infection, or the back-door/vulnerability that caused the infection, onto this new site.
There is no Software/Firewall that can protect your website from an infection that is placed there by a system admin.
To help you sort out this issue and find the active cause of this infection I would need to see the files on the infected site(s). Can you send me a link to the websites that are currently not working and maybe include the error_log files from the server?
You can email me directly with any private or otherwise sensitive data: eli AT gotmls DOT net
