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Yep, found it in ‘footer.php’. I saved the hacked file as footer.txt and put it in http://www.freebyu.org/temp/footer.txt
You can have a look at it there if you want to see how they juked you malware detector. The malicious code is loaded from a different URL, in a chunk of code buried in the middle of a lengthy php comment.
How in the world could they have gained access to the text of footer.php? Could they have done that from the admin backend if they had a username? Or would they have had to hack into the server filesystem itself?