In as much as the rotor (if you had it off) has no spacers between itself and the wheel spider, that would lead me to believe that you've forgotten the spacer that goes between the caliper bracket and the and the wheel. You have wheel, spacer, barcket and then swingarm.
If the rotor is rubbing the pads a bit, that's ok. The first application of the brakes will center the pads anyway. Pad to rotor clearance is a direct result of the puck seals resisting the outward movement of the pads.