Once you remove the rust with acid (vinegar) you have to rinse thoroughly, dry and protect the bare metal with wax or an oil film. (at least until you're ready to touch up with paint). I also do a rinse with baking soda & water to neutralize any remaining acid, but I don't know if it's necessary if rinsed well enough.

As for the fork (singular, the same as the one you eat with), vinegar won't etch out the metal enough to affect the texture. The so-called groves are actually emboss marks from the serrations in the QR, and even if sanded smooth (would take a while), would be pressed back in by the skewer, assuming you're using the same one.