Simple, you just need to re-index the barrel in the upper receiver socket to zero out the bore with the focal line of sights center (or to what you perceive center).
One method is to re-install the barrel to the needed front sight to bore line idex, with another to just drift the entire barrel in the upper socket by firmly holding onto the receiver only, and striking the front sight base just above the barrel with a leather mallet (read non-maring) to slip the entire barrel in the upper receiver socket ,via the impact torque.
As for the carry handle attachment sights being marked 3/6, this is simpley due to the fact that the sight can not be raised as high as a fixed handle sight (a-2) due to the shorter elevation screw used on the sights(read the elevation screw is shorter since it can not be lowered into the receiver area/flat top rib.
P.S. this really should have been posted in the trouble shooting or building forum, but since I'm here, what the hell.