This is a huge help. I spent some time yesterday going through the site and updating my links to https where possible. Those don't all appear to have indexed yet. The bit about the timthumb exploit is particularly helpful. My theme lets me disable that, and I can get rid of the timthumb php file. I'm still concerned that sitelock could be exaggerating the problem though, we started having these issues with google around when it was implemented.
Best posts made by laidlaw1
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RE: Homepage refusing to show up in Google (rest of pages fine)