At least you know why you have this problem :thumbs:
I'd just clean the spindle mating surface and install the new rotor, then measure runout. If it's not all that much - maybe you're lucky like I was - and the runout is ok. If it needs a .002" shim I'd try to clean up the mating surfaces a little more, maybe with a DA grinder or a sander... 60 grit should do the trick, you only need to remove .001" on the spindle to change the runout on the larger diameter rotor by .003" or .004"..... . You can do that once the studs are removed, just bolt the rotor on using the 3/8" bolts that replace the rivets.
Replace the wheel studs with Moroso or ARP stuff.