Dear Léa,
May I suggest something? Your application is extremely ambitious and difficult. This is why I'd suggest you to proceed step-by-step, starting first from a good hydrodynamics solution (T3D), then move to only waves and currents (T3D+TOM), then start some simple tests only currents and sediment transport (T3D + Gaia), then include waves, and at the very end of the chain, couple everything with Nestor.
I know that we always want to attack the whole problem from the start, but this kind of multi-physics/multi-scale approach only succeed with you'are advancing 'in blocks', if not, most of cases is failure guaranteed.
All the success with your nice application,
Best wishes,
Pablo