From what I see in the first 2 pics big D is that 1,2,4 look OK and that its only 3 thats out. Which is good,its pipe is connected to # 2 by the crossover,which means it can be moved in or out.Go ahead and bend it without putting any pressure on any welds. You'll need to hold 3's pipe indepedantly of the rest of the system while adjusting.I've put on a few exhaust systems over the years and rarely do they NOT require tweaking.
RSD.
RSD.