Production planning of final assembly systems is a challenging task, as the often fluctuating order volumes require flexible solutions. Besides, the calculated plans need to be robust against the process-level disturbances and stochastic nature of some parameters like manual processing times or machine availability. In the paper, a simulation-based optimisation method is proposed that utilises lower level shop floor data to calculate robust production plans for final assembly lines of a flexible, multi-stage production system. In order to minimise the idle times when executing the plans, the capacity control that specifies the proper operator-task assignments is also determined. The analysed multi-stage system is operated with a pull strategy, which means that the production at the final assembly lines generates demands for the preceding stages providing the assembled components. In order to guarantee the feasibility of the plans calculated for the final assembly lines, a decomposition approach is proposed to optimise the production plan of preceding stages. By this way, the robust production can be ensured resulting in reduced losses and overall production costs even though the system is exposed to changes and disturbances.