Do you know if the lights worked before you replaced the wiring? A bad turn signal switch can mess up both the turn signal and brake lights on one side. But check all other continuity issues in the rear first.
Have to ask, you do have the correct bulbs, probably 1157 if using original incandescent, with the two contacts in the base and the tail light sockets have two contacts in them? (The backup light should have one contact and use an 1156.)