So, I have simply changed ownership of everything in the Doc Root directory to be owned by root:root. The directory itself also changed to root:root ownership. Hopefully that's the end of that!
Just thought I would pass it on. I have had most of these sites up for almost year in the apache:apache configuration. Guess I am just too trusting! Security by obscurity will always eventually fail I suppose.
So-- fair warning. Change your file ownerships to someone other than apache!