Put in some amg fender spacers aka home depot nylon washers, the advantage is the fenders will look flared.

Chances are it rubs because the suspension is slightly different than before, by that I mean, try new control arms bushings.

Ask the shop for a tad of touch up paint and apply it, they won't respray it unless they are in a real good mood.

In all likelihood, the bumper mount or the fender bracket is slightly bent and that's why it's misaligned, I say about an hour's worth of fine tuning.