if you have a own server; restrict ftp access to certain IPs. that will help a lot.
define the default document in IIS, remove unnecessary default documents for a site
check the program code properly for sql injection possibility.
by the way,
create a new folder and configure the site when you out the site again.
have a good antivirus [like symantec end point protection] that detects unauthorized entries and injections.
hope this helps