Ok i done the fud flap mod a long time ago. And i still have those holes and my truck is going into a body shop. IM cool with the owner and he said it would be reatrded to shave those holes. So what are those plus you can buy? I told him about him and he said it would paint them with the paint on the bumper.
You can buy the plastic push plugs in packs at an auto parts store (cheap) or individually at the Ford dealer (not). Slang name often used is "christmas trees". They are available in several diameters, so be sure they fit the holes properly before painting them.