NASA’s James Webb Space Telescope (JWST) is a 6.6m diameter, segmented, deployable telescope for cryogenic IR space astronomy. The JWST Observatory architecture includes the Optical Telescope Element (OTE) and the Integrated Science Instrument Module (ISIM) element which contains four science instruments (SI), including a guider. The SIs and guider are mounted to a composite metering structure with outer envelope approximate measurements of 2.2x2.2x1.7m. These SI units are integrated to the ISIM structure and optically tested at NASA Goddard Space Flight Center as an instrument suite using an Optical telescope element SIMulator (OSIM). OSIM is a high-fidelity, cryogenic JWST simulator that features a ~1.5m diameter powered mirror. The SIs are aligned to the flight structure’s coordinate system under ambient, clean room conditions using opto-mechanical metrology and customized interfaces. OSIM is aligned to the ISIM mechanical coordinate system at the cryogenic operating temperature via internal mechanisms and feedback from alignment sensors and metrology in six degrees of freedom. SI performance, including focus, pupil shear, pupil roll, boresight, wavefront error, and image quality, is evaluated at the operating temperature using OSIM. This work reports on the as-run ambient assembly and ambient alignment steps for the flight ISIM, including SI interface fixtures and customization and kinematic mount adjustment. The ISIM alignment plan consists of multiple steps to meet the “absolute” alignment requirements of the SIs and OSIM to the flight coordinate system. In this paper, we focus on key aspects of absolute, optical-mechanical alignment. We discuss various metrology and alignment techniques. In addition, we summarize our approach for dealing with and the results of ground-test factors, such as gravity.