If the spacers were incorrect you would not have the calipers and brake pads correctly centered. IF that's the case, it will cause too much brake resistance on the rotor and the heat will eventually warp the rotor. Floating rotors will work for a while but they too will eventually warp if the centering/resistance is incorrect. A warped rotor will usually cause uneven wear on one side of a set of brake pads - usually completely wearing down one pad while the other pad shows normal wear. It's an indication of what side of the rotor has the run-out. If this is the problem you may have seen an abnormal amount of brake dust on the affected wheel. I hope you have figured this out by seeking the opinion of an experienced mechanic. If the rotor has warped, a good mechanic ought to be able to re-true the rotor [on the wheel in a jib] and save you a bit of money as opposed to replacing it. I've seen rotors re-trued by my mechanic. It's pretty impressive to see this level of experience but it is an option with the right mechanic who can actually lace and true wheels.
Old-school Harley mechanics are getting scarce.
