The local structure, atomic and magnetic structure correlated over a small length scale, of a material has a strong impact on material properties. Pair distribution function (PDF) analysis is a strong tool to investigate local structure and magnetism of this nature. This work outlines extensions to current one dimensional magnetic pair distribution functions (1D-mPDF) and the fitting of structures with symmetry breaking local atomic distortions. 1DmPDF analysis has been used to study local magnetic structure, but requires a rotational averaging of the correlations so directional information is lost, as in powder diffraction experiments. Three dimensional difference magnetic pair distribution function (3D-∆mPDF) analysis does not require this rotational averaging and preserves directional information. This is a useful tool in analyzing experimental data like single crystal neutron diffraction and studying locally anisoptropic magnetic structures. Here we present a technique and software tools to calculate the 3D-∆mPDF pattern of a given structure and give a brief analysis of the local magnetic structure of MnTe. Another problem in PDF analysis is the modeling of structures with symmetry breaking local atomic distortions. Symmetry-adapted distortion modes have been used for structural refinement in Rietveld refinement for at least 10 years; more more recently, this has also been applied to PDF data. We present here a detailed discussion of the use of symmetry-adapted modes for structural refinement using PDF data. We also outline new open-sourced software tools to apply this technique and show two analyses using symmetry-adapted structural modes.