The Compact Linear Collider (CLIC) provides a path to a multi-TeV accelerator to explore the energy frontier of High Energy Physics. Its two-beam accelerator (TBA) concept envisions complex 3D structures, which must be modeled to high accuracy so that simulation results can be directly used to prepare CAD drawings for machining. The required simulations include not only the fundamental mode properties of the accelerating structures but also the Power Extraction and Transfer Structure (PETS), as well as the coupling between the two systems. Time-domain simulations will be performed to understand pulse formation, wakefield damping, fundamental power transfer and wakefield coupling in these structures. Applying SLAC's parallel finite element code suite, these large-scale problems will be solved on some of the largest supercomputers available. The results will help to identify potential issues and provide new insights on the design, leading to further improvements on the novel two-beam accelerator scheme. Show Partial Abstract