I am installing a rear disc setup on my 9". I placed the rotor on the flange, lugged it down, and setup a dial indicator touching the pad surface of the rotor. When I rotated the differential, the rotor showed 0.04" out of square. I then rotated the rotor relative to the axle and checked it again to see if the rotor or the axle flange was causing the problem. It's the alxe flange.

What should i do? Should I shim in between the rotor and the flange?