This paper demonstrates the stability limits of a human-in-the-loop closed loop control system, where the plant to be controlled has redundant actuators with uncertain dynamics. The human operator is modeled as a general transfer function, unlike earlier work where specific filters are associated with human reactions. This helps with developing a more general stability analysis, and earlier studies can be considered as special cases of the proposed framework in this paper. Adaptive control allocation is employed to distribute control signals among redundant actuators. A sliding mode controller with a time-varying sliding surface provides desired control inputs to the control allocator. A flight control task, where the pilot controls the pitch angle via a pitch rate stick input is simulated to demonstrate the accuracy of the stability analysis. The Aerodata Model in Research Environment is used as the uncertain, over-actuated aircraft model.