We carry out a realistic simulation of Majorana nanowires in order to understand the latest high-quality experimental data [H. Zhang et al., arXiv: 1603.04069 (2016)] and, in the process, develop a comprehensive picture for what physical mechanisms may be operational in realistic nanowires leading to discrepancies between minimal theory and experimental observations (e.g., weakness and broadening of the zero-bias peak and breaking of particle-hole symmetry). Our focus is on understanding specific intriguing features in the data, and our goal is to establish matters of principle controlling the physics of the best possible nanowires available in current experiments. We identify dissipation, finite temperature, multi-sub-band effects, and the finite tunnel barrier as the four most important physical mechanisms controlling the zero-bias conductance peak. Our theoretical results including these realistic effects agree well with the best available experimental data in ballistic nanowires.