The Wendelstein 7-X modular advanced stellarator is in the commissioning phase at the Max Planck Institute for Plasma Physics in Greifswald, Germany. The focus of the numerical analysis has been shifted from support of the machine design and assembly toward preparation of the commissioning steps, assessment of possible field disturbances under operational loads, and exploration of operational limits. This paper emphasizes on the development, evolution, and realization of new analysis strategies, as well as on implemented numerical approaches for electromagnetic, thermal, and structural analyses. Remarkable results of the first comparisons with measurements from the extended mechanical instrumentation system are presented in detail and cover evacuation/flooding of the cryostat and plasma vessel, the first cooldown of the magnet system (MS), and both the superconducting coil groups and integral MS commissioning. Finally, some lessons learned during the transition phase are highlighted, which might be relevant for other large fusion machines.