If the chain and both sprockets line up and there is no strange wobble or noises when you ride it, then it has to be something with the fender. As to the scars on the tire, check how far the 2 bolts on the chrome supports protrude beyond the weld nuts on the inside. A sissy bar or a luggage rack or both require 2 additional chrome supports over the fender supports and also longer bolts. If the previous owner removed those parts and reinstalled the same long bolts, riding 2 up or hitting a bad bump with a soft shock setting would allow those bolts to contact the rear tire. I have an 03 TA - don't ask how I know these things....
