Two significant challenges facing functional electrical stimulation (FES) cycling are the low power output and early onset of muscle fatigue, mainly due to the non-physiological and superficial recruitment of motor units and weakness of the antagonistic muscles. Thus optimization of the cycling biomechanical properties and stimulation pattern to achieve maximum output power with minimum applied electrical stimulus is of great importance. To find the optimal seating position and stimulation pattern, the previous works either ignored the muscle's force-velocity and force-length properties or employed complicated muscle models which was a massive barrier to clinical experiments. In this work, an easy-to-use and precise muscle model in conjunction with Jacobian-based torque transfer functions were adopted to determine the optimal seating position, trunk angle, crank arm length, and stimulation intervals. Furthermore, the impact of muscle force-velocity factor in finding the optimal seating position and stimulation intervals was investigated. The simulation models showed the trivial effect of the force-velocity factor on the resulting optimal seating position of six healthy simulated subjects. This method can enhance the FES-cycling performance and shorten the time-consuming process of muscle model identification for optimization purposes.