can you get a picture of what you are talking about. I've fixed drip rails before, and your can buy new ones at several venders.
The pin holes are only pin holes on the surface. They will be craters after you drill them out.
You may be better off getting a new cab roof and drip rails.
I hope you weren't planning on plugging the pin holes with bondo. you never want to fill a hole with bondo. They should be welded.
Frank