Kelsey Hayes longer wheel studs

You could also have the stud heads turned down about a 1/16" or so on the under side rather than counter bore the hub.

Modification of the hub wouldn't be an option. The rotor doesn't go over the hub, it mounts to the back. Any modification to the back of the hub would change the rotor location. The only modification I could see possible would be the inside of the rotor but I wouldn't do that either.