The reliability of solid oxide fuel cell (SOFC) systems is closing the gap to meet the requirements for market implementation. However, with the recent advances of the technology, the lifetime of SOFC stacks is becoming increasingly limited by mechanical failures, which need to be overcome for lowering costs. Numerical thermo-mechanical investigations are relevant to understand and predict potential failure modes in SOFC stacks, because of the complexity induced by the variety in materials, local conditions and effect of history. Standard finite-element (FE) stack modelling approaches commonly consider idealised components, i.e. computational domains imported from computer-aided design. To further advance the understanding of mechanical failure in the light of cost reductions, statistical variability in the dimensions and geometry of the produced stack components - because of imperfections in the manufacturing processes - must be accounted for. This study is focused on the effects of variability in the flatness of the metallic interconnect (MIC) on the distribution of the contact pressure over the active area. The component initial deformations are included in a 3-D thermo-mechanical model of a series of single repeating units (SRUs). The anisotropic elastic and creep properties of the gas-diffusion layer (GDL) materials are estimated by computational homogenization. This allows the modelling of the GDLs as simplified continuum geometries to reduce the stack simulation runtime. The stack conditioning procedure is simulated to account for the effects of the stack manufacturing on the stress-state before operation. After this initialisation step, the simulation of stack operation consists in importing temperature profiles from thermoelectrochemical simulations into the FE thermo-mechanical model. The simulated operation scenario is long-term polarisation in co-flow configuration, interrupted by thermal cycles. The simulation results show that MIC pre-deformation cause a less uniform distribution of the contact pressure over the active area. Thermal cycling at the beginning of operation appears as the most critical situation (based on inspection of the contact pressure). The situation tends to improve during prolonged polarisation.