When your site was hacked .. some malicious code was added to one of the php files somewhere in your site, it could be in the core wp files, in a plugin or in the theme any files that get loaded to generate your website each time a page is loaded.
Probably the theme, as if you did a fresh install of wordpress and deleted all the plugins you might fix the problem but your less likely to change your theme.
Usually these hacks are use obfuscation (like encryption) to try and hide the code more and prevent you from figuring out what that line(s) of code actually do.
something like
`<?php eval(base64_decode(“……… gibberish, HEX or binary ………”)); ?>’
so scanners like the two mentioned above will look in every file in you site for php functions like ‘eval’, ‘base64_decode’ etc which are commonly used to hide, obfuscate code, as these no real reason to do it unless your trying to hide what your up to.
They should then give you a report of everything it found that it considers suspicious. You’ll then have to investigate manually.
You can also ftp to your site and look at the date modified of the files in your theme, they should all have roughly the same date, i.e. when it was installed or updated, any file with a newer date has be tampered with or modified.
Another option is to try a clean install, back up you site.
make a list of all you plugins, download fresh clean copied from the wp.org, download a fresh copy of wordpress, and a fresh copy of your theme, from a reputable source…
set up you site completely fresh, extract wordpress, put the new plugins in the plugins folder same for the theme, then copy over the old uploads folder i.e. wp-content/uploads probably wise to do a quick visual check there should only uploads in this folder imgs etc… defiantly not scripts .php etc..
finally copy over your wp-config.php
file but first scan it for anything that looks malicious, look at ‘wp-config-sample.php’ to get an idea what looks right and what look wrong.
Hope that helps