Sorry you're having to do the cleanup by hand. That sucks big time.
As an aside, as someone with a LOT of domains, the fact that your host wasn't offering a free or low cost virus scan just to protect themselves doesn't say positive things about them.
Tell me about it. We've been with HostMonster for almost 20 years and I would have thought THAT alone would have meant something. We went several rounds on Thursday and yesterday about it with the security support team. I strongly feel this came from their end and they should have been responsible. However, when dealing with low cost hosting they want to nickel and dime you for everything. I did threaten them to leave for HostGator but she got me there because the company also does security for them, too. *rolls eyes*.
That being said, because we've been with them almost 20 years, this is the first time something like this has happened so I feel stuck between a rock and a hard place because, while yes, we've had the occasional outage here and there, this is the first MAJOR issue I've had with them.
For those site I could, I already have a free firewall in place. It won't stop everything but it's better than having nothing at all. I do need to figure something out for the boards, though. I'll skim UBB to see if we can put something in place that doesn't cost us $300.
Thanks!