I don't know what bars you have on your bike but : after putting 12 1/2 apes on my bike it looked like the whole situation was out of line. I road it that way til I couldn't stand it any more. I then replaced the riser bushings with urethane bushings and it fixed the problem. Just a little wear of the OEM bushings (rubber) will give a different view of alignment. JMO.
11 FLTRU 103 Red Hot Sunglow
Rush Full System 2:1,Air ride,Madstad,WO 614B, SE 255 cams, Ventilator,bunch of other stuff