The calibration of high-energy X-ray diffraction setups using an area detector and a rotation axis is discussed. The characterization of the tilt and spatial distortions of an area detector was discussed in part one of this series [Borbely, Renversade, Kenesei & Wright (2014). J. Appl. Cryst. 47, 1042-1053]. Part II links the detector frame to the laboratory frame comprising an additional rotation axis and introduces a general diffractometer equation accounting for all sources of misalignment. Additionally, an independent high-accuracy method for the evaluation of the crystallographic orientation and cell parameters of the undeformed reference crystal is presented. Setup misalignments are mainly described in terms of a residual strain tensor, considered as a quality label of the diffractometer. The method is exemplified using data sets acquired at beamlines ID11 (European Synchrotron Radiation Facility) and 1-ID (Advanced Photon Source) on Al and W single crystals, respectively. The results show that the residual strain tensor is mainly determined by the detector spatial distortion, and values as small as 1-2 x 10(-4) can be practically achieved. (C) 2014 International Union of Crystallography