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I got this trojan today on my main pc. Good grief, I've been working on this problem for the past 4 hours.
It evidently utilized the way I had WinSCP set up and added some Js to every index* and *.js file on all my sites. sigh . Guess who will not be storing passwords in WinSCP from now on?
As soon as I realized what had happened I deleted whole directories as soon as possible. I checked every file by modification date, ... and on and on. I'm still checking things but I "think" I have it taken care of.
For tools, I used MalwareBytes and HiJackThis.