I've just removed the studs by refitting the wheel nuts and using a rubber mallet to gently tap around the flats, then the end and repeating this process until they incrementally drifted out. None of them were particularly stubborn so I don't think I've introduced any more distortion into the flange.
I've put a steel rule across the hub and boy, were you right, Pete! Across a central plane, the flanges of the hub are set back from the centre, giving over 1mm of see-saw action when I locate the drum on the hub. This explains why the old drum was cracked with the wheel bolts torqued down!
Not something a file is going to help with and now I'm wondering if its beyond repair...