Wilwood rear disc help.......

Sounds like the shoulder on the wheel studs is larger than the holes for the wheel studs in the rotor?

If that’s the case, DO NOT alter the studs. The right way to do it would be to ream the holes in the rotor until the rotor sits flush against the axle flange. Other option would be to drill them slightly larger, the smallest you can make them and have them clear would be best. As long as the axle register matches the hub bore in the rotor having the wheel stud holes slightly larger shouldn’t hurt anything, it won’t move when everything is tightened. Having the rotor flush against the axle flange is very important.

But that assumes the rotor isn’t hanging up on something else. The other usual culprit is the center register on the axle. Same deal, leave the axle alone and have the rotor clearanced. Harder than the wheel stud issue though, if it’s more than what you want to take out with some sandpaper the center hole should be machined so it stays concentric to the axle register.