cpt,
You don't mention where on the blade the marks are, and if they have any appreciable depth to them. What size are they? Have you looked at them with a 5 or 10X maginfier? I don't know what protective coating you refer to, is it the black paint?
The black marks on the trailing edge of the stabilizer could be simple static discharge spark trails, which have fairly high voltage. They can be prevented by adding back the static wicks, I think. I seriously doubt that a crew could not recognize a lightning strike.
thanks,
Nick