Same issue with a site I manage as well.
We saw that Google had marked the site as containing malicious files, and so I took a look at the ftp to find the same files and issues as mentioned in this forum.
I've gone in and removed every change I could find by looking at the timestamps. Every file that had an issue all had a matching timestamp, so this was the clue to finding all of the issues.
Now that I've removed every issue I could find, as well as using the suggestions mentioned above by Jan Dembowski, I submitted to google in Webmaster Tools, a request for them to check the site again, and release the "This site contains malicious ..." warning.
The wait may be up to 24 hours for them to review it, but hopefully, we'll be in the clear.
I'll report back here if there are any other hoops I have to jump through.