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This study aims to optimize the throughput and cycle time of a pull type multi-product, multi-line and multi-stage flexible manufacturing system whose resources are subject to breakdown conditions. To ensure a continual supply of the finished products, under breakdown conditions, the parts/ materials flow through alternate routes exhibiting routing flexibility. Every machining and assembly station is equipped with automated inspection units to inspect the quality of the products. The system is modeled through colored Petri net methodology (CPN) and the impact of input factors is shown on throughput and cycle time of the system. The study explores multi-factor optimization of the system using design of experiment (DoE) and response surface methods.