In Line-less Mobile Assembly Systems (LMAS) the mobilization of assembly resources and products enables rapid physical system reconfigurations to increase flexibility and adaptability. The clean-floor approach discards fixed anchor points, so that assembly resources such as mobile robots and automated guided vehicles transporting products can adapt to new product requirements and form new assembly processes without specific layout restrictions. An associated challenge is spatial referencing between mobile resources and product tolerances. Due to the missing fixed points, there is a need for more positioning data to locate and navigate assembly resources. Distributed large-scale metrology systems offer the capability to cover a wide shop floor area and obtain positioning data from several resources simultaneously with uncertainties in the submillimeter range. The positioning of transmitter units of these systems becomes a demanding task taking visibility during dynamic processes and configuration-dependent measurement uncertainty into account. This paper presents a novel approach to optimize the position configuration of distributed large-scale metrology systems by minimizing the measurement uncertainty for dynamic assembly processes. For this purpose, a particle-swarm-optimization algorithm has been implemented. The results show that the algorithm is capable of determining suitable transmitter positions by finding global optima in the assembly station search space verified by applying brute-force method in simulation.