"noticed the the bottom of the rotor (assume you meant caliper) rubbing on the new rotor." the caliper mounting is in a fixed position, relative to the backing plate and the center of the spindle, so no amount of rotor adjusting will make up for the lack of taper on the new rotor which hits the caliper. the bearing wedged on the spindle is another problem, in regard to the new bearing either being located on a different position on the spindle, the race seated in a different position inside new rotor or the wrong inner bearing id. it might be fixed with a another bearing, or move the race to a position so the bearing does not wedge on the spindle. this is all trial and error, and not likely to work properly unless you fix the rubbing of the rotor on the caliper. machine shop could properly turn rotor to get clearance, but that would void any warranty on that rotor if there was one. IMO, your old rotors if not warped, don't look too thin to me. don't turn them, if grooved, so what, some people pay big money for grooved rotors, your new pads will quickly match those grooves, and pads are cheaper than any of the other parts or machine work. pads don't have rivets these days, so no more grooves anyway. you will actually have more contact surface.