Thanks. It looks like it crawled through all the directories automatically, sequentially over a period of about an hour. It only touched the one domain on our server as far as we can tell. They must not have been too good of hackers, as they did not reset back the times on the changed files, which is how I discovered it. Otherwise it may have been months before we discovered it.
I had a nasty virus on my computer last week which I finally got rid of with some help, but this just happened yesterday.