I recently came across this plugin for wordpress. Just cleaned a site with over 1500 infected files. I ran a small scan and then checked one of the files for processing. It seems to use sed (possibly) to remove the infected line in the files. It keeps a log of all files it cleaned but I’m not sure where it quarantines these. Anyway, it’s really helped me out. I ended up backing the entire site, then clicking the ‘automatically fix all files’ button. Whilst it took a while to do and it did this in batches, it fixed all the files on that site. Very happy with it.