Well, here's the situation...

First and foremost, EVERYONE you need to make sure you keep updated with wordpress, shopping carts, CMS's, etc. This is how whatever we have got in according to National Net.
If you host multiple sites on 1 hosting platform, everything hosted and any files you have on that 1 platform can get infected very fast even within minutes if not seconds.

We're getting closer to being finished but about another several days to go to only finish the scan. We have close to a million files on the server, if not more. So as you see this is very tedious.