I've had similar issues in past. It is not just the obvious code that creates the problem, it is the sleeper files that put so far into your file structures.
What does host say?
If you want another server manager to eradicate all the shit hit up Chris from admin at way3 dut com and tell him the guy who owns videostripgames.com said you may be able to help.
How many sites do you have on the server, because it will likely effect them all. My breaches always stemmed from wordpress vulnerability.
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