I remember my history teacher making bullet holes in a model jeep by heating a pin with a soldering iron and forcing it through the plastic. It looked good. Just be VERY careful or you'll burn off your finger prints.
If you don't want Legion or NCR graffiti. The Brotherhood seem everywhere. You've got some raiders - easy enough to come up with a gang name. Then there are the generic ones like No Mutants/No Ghouls/No Smoothskins/No Whatever... Danger: Deathclaws/Mirelurks that fantastic Nuclear symbol that I really should know the name of..?