Thanks John. Definitely not factory...A/C drain holes gets my vote.
I am thinking it was factory.... look at this photo
http://inlinethumb55.webshots.com/45302/2702918180103882008S600x600Q85.jpg that's factory applied sound deadener, right? The metal under the sound deadener was pristine, as if the tar type material was sprayed on it shortly after the cab was assembled.
If the holes are under the factory applied sound deadner how can the holes not also be factory applied?