Electron pair distribution function (ePDF), combined with four-dimensional scanning transmission electron microscopy (4D-STEM), provides a powerful approach for uncovering detailed information about the local atomic structure and structural variations in disordered materials. However, achieving high accuracy in ePDF analysis requires careful control of experimental and instrumental parameters. In this study, we systematically investigate the effects of key electron optical and measurement parameters on ePDF analysis using simulations as the primary tool, complemented by experimental validation. Specifically, we examine the influence of diffraction angle range, beam convergence semi-angle, detector pixel resolution, sample thickness (multiple scattering effect), noise, and electron beam precession on the resulting ePDF. By integrating multi-slice electron diffraction simulations with experimental diffraction data, we identify optimal conditions for accurate ePDF extraction and provide practical guidelines to improve analysis precision and reliability. These insights contribute to refining ePDF techniques, particularly for applications involving amorphous and nanostructured materials.