Tim, you can try oxalic acid that is available in the paint department of most home centers. This shold get out most if not all of the black marks. Use the Oxalic acid according to label directions and then neutralize with 1 cup of household bleach to a gallon of water, then rinse with fresh water. Since you will be putting water on unfinished wood, you will have to lightly sand to remove the raised grain. A well used sanding disk on a buffer is sufficient for this after the wood has dried completely. No need to drum sand the whole floor again.