...try looking for "REFRESH" or "HTTP-EQUIV"
I know you don't know me but if you would like help I would be glad to try to help but the only I could do that is to get access to your database. I am very curious how they did this for the tool I am coding hence my interest.
EDIT: you are searching like this, right:
%refresh%
%http-equiv%
%index4_files%
I ask as I get hits for the first two and my site is not hacked. But there are not may of them so you can look at them to find the cause.
Also search for this if you are not finding anything...
%base64%
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