I have been affected by this virus/malware and currently cleaning up. I hope this will be helpful:
1) You most likely have a TROJAN on your PC. To verify this simply run (Start > Run... or Windows key + R) and type "cmd" or "regedit". If either of those doesnt open its window as expected, you have the Js:Redirector trojan. You can also verify that the anti virus programs aVast and Malware Bytes can not connect to updates for some reason (sneaky trojan that is). Plus, you'll notice that the Security program of the Control Panel was disabled, you wouldn't have seen a notification in the tray icons to tell you that the virus protection was disabled.
2) This is a very recent exploit, apparently of vulnerabilities inflash or pdf plugins, thus you are not safe even if you didn't use Internet Explorer!
As for me, I believe because I hate programs slowing down my PC, I have my Windows Updates on "manual", and I didn't have resident protection (scanning of all web connections, etc), and I was probably infected by visiting another hacked site which was not blacklisted yet. Also I was over confident in non-IE browsers! I sometimes ignore the blacklist warning as I am curious about what the scripts do etc, and forgot once again just how BAD Windows really is. Conclusion: leave Windows Updates on automatic, have minimal resident protection (aVast Web Shield + Network Shield).
3) Because this is a trojan that sends back your FTP password, it doesn't matter how good your password was!
4) Try to lceanup your PC with Malware or aVast, it will find a file ending with ".ctv"
You MUST have a virus database dated 14 May or more recent. If you can't update (as explained above), then follow these instructions (you'll need to extrapolate but basically you have a file, the name may vary, which is pointed in the registry, and use HiJackThis to remove it, once you rebout without this file excuted, all is fine)
5) Of course update your passwords, BUT make sure the trojan is removed first!
6) For an exact list of all pages modified try to get a FTP log and you'll find the IP of the script/hacker and all touched files.
7) If you have a complete local copy of the "production" environment, then the safest is to delete ALL the site on the server, and re-upload all files.
8) During the clean up process DONT visit your infected site, or you will re-install the trojan! If you have the latest aVast Home Edition and the "Web Shield" protection it will give you a warning and block the page from being executed by your browser.