NASA's James Webb Space Telescope (JWST) is a 6.5m diameter, segmented, deployable telescope for cryogenic IR space astronomy. The JWST Observatory includes the Optical Telescope Element (OTE) and the Integrated Science Instrument Module (ISIM), that contains four science instruments (SI) and the Fine Guidance Sensor (FGS). The SIs are mounted to a composite metering structure. The SIs and FGS were integrated to the ISIM structure and optically tested at NASA's Goddard Space Flight Center using the Optical Telescope Element SIMulator (OSIM). OSIM is a full-field, cryogenic JWST telescope simulator. SI performance, including alignment and wavefront error, was evaluated using OSIM. We describe test and analysis methods for optical performance verification of the ISIM Element, with an emphasis on the processes used to plan and execute the test. The complexity of ISIM and OSIM drove us to develop a software tool for test planning that allows for configuration control of observations, implementation of associated scripts, and management of hardware and software limits and constraints, as well as tools for rapid data evaluation, and flexible re-planning in response to the unexpected. As examples of our test and analysis approach, we discuss how factors such as the ground test thermal environment are compensated in alignment. We describe how these innovative methods for test planning and execution and post-test analysis were instrumental in the verification program for the ISIM element, with enough information to allow the reader to consider these innovations and lessons learned in this successful effort in their future testing for other programs.