xj8 2002 restoration

Can anyone help with a rust problem? I have recently bought a replacement O/S/F wing which is in a very good condition generally but there are some rust spots that need to be attended to. I have stripped the small areas(around the wheel arches), down to the metal there is no sign of any brown rust but there are some dark, almost black indentations still present. My question is, "should I rub down until these spot are completely gone"?

Out of interest I did manage to get a GRP wing for the N/S. But the company that manufactured this has gone since covid and I've not been able to find another.