The objective of this study is to model and maximize performance of an integrated Automated Guided Vehicle System (AGVS), which is embedded in a pull type multi-product, multi-stage and multi-line flexible manufacturing system (FMS). This study examines the impact of guide-path flexibility on system performance through the development of three different guide-path configurations which range from dedicated to flexible relationships between automated guided vehicles (AGVs) and machine/assembly station resources. The system is modelled using coloured Petri net method (CPN) and the simulation results lead to identify the resource redundancy which can be rectified to achieve lower overall cost of the system through the development of flexible guide-path configurations. The study is extended to seek global near-optimal conditions for each guide-path configuration using response surface method, which yields improvements in system throughput and cycle time along with a decrease in the numbers of AGVs.