headliner repair?

In all likelyhood, the holes you describe are from mice in your headliner. It would probably be your best bet to completely replace the headliner. And when you remove the old one, you can clean anything left over of the nest and clean it good with a disinfectant. That way, when you take your car out for a drive on a warm day, you won't be getting any "colorful" odors!!!!!!