In this paper,an optimal operational strategy is developed to maximize the throughput rate from a finite capacity integrated assembly line system (consisting of a set of tandem workstations, a set of inspection stations, a loading station and an unloading station, linked by a set of transporter stations) while controlling both the bottleneck and the flow time. To develop an optimal operational strategy, a stochastic optimization model is developed and a closed form solution is derived to maximize the throughput rate from the system such that the resulting probability of finding either a workstation or a transporter station blocked is sufficiently close to zero, and the resulting probability of spending time by an arbitrary workpiece either at a workstation or at a transporter station in excess of a desirable value, is sufficiently close to zero.