The beam formation and acceleration of the ITER neutral beam injector will be studied in the full-scale ion source, Source for Production of Ions of Deuterium Extracted from a RF plasma (SPIDER). It will be able to sustain 40 A deuterium ion beam during 1-h pulses. The operating conditions of its multi-aperture electrodes will diverge from ideality, as a consequence of inhomogeneous heating and thermally induced deformations in the support structure of the extraction and acceleration grids, which operate at different temperatures. Meeting the requirements on the aperture alignment and distance between the grids with such a large number of apertures (1280) and the huge support structures constitute a challenge. Examination of the structure thermal deformation in transient and steady conditions has been carried out, evaluating their effect on the beam performance: the paper describes the analyses and the solutions proposed to mitigate detrimental effects.