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 towards preparation of commissioning steps, assessment of possible field disturbances under operational loads, and exploration of operational limits. The 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 first comparisons with measurements from the extended mechanical instrumentation system obtained during evacuation and flooding of the cryostat, the first cool-down of the magnet system and also during first part of the superconducting coil groups commissioning are presented in detail. Finally, some lessons learned during the transition phase are highlighted which might be relevant for other large fusion machines.