Modern and future observation Space missions face increasingly more demanding pointing performance requirements. This is accompanied with the development of larger lightweight flexible structures. This paper outlines a methodology for modeling a generic multi-body flexible spacecraft in an end-to-end fashion within the Two-Inputs Two-Outputs Port framework: from disturbance all the way to pointing performance by tacking into account all the uncertainties of each sub-system. A particular focus is dedicated to a novel generic model for Solar Drive Array Mechanisms and its harmonic disturbances produced by the micro-stepping driver and the gearbox imperfections. The proposed model is validated with the on-board telemetries of a European spacecraft. Moreover this paper shows how the proposed model-based approach can be easily used for control design and closed-loop robust performance analysis. Worst-case scenarios of mechanical parameters combination are investigated to provide robust performance certificate of the reference study case. A Linear Parameter-Varying observer, scheduled by the solar array rotor angle, is finally proposed in order to estimate the disturbance torques induced by the gearbox imperfections just using the measurements coming from a classical attitude control system: a star tracker and a gyrometer.