it is hard to tell from the pic, but it looks like the outer pad is wedged in there crooked, and that is causing the rotor to not sit flush. I would back up a little and take the caliper off. First lay a straight edge across the wheel studs and measure to the bracket that the caliper rests on (front and rear), they should be the same I think. Then check to make sure the rotor sits flush against the inside of the axle. Then put the caliper on without the pads to see if the rotor sits flush still and measureto see if it is even on both sides. It doesnt have to be the same distance on both sides of the caliper, just even on the same sides front and rear if that make sense. Then try with the pads, and do the same thing.
From the pic though it just looks like the outside pad is wedged in there incorrectly. If all that fails post some more pics of different angles and let us know exactly what set up you are using. Good luck!
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