The exact numerical solution of the nonlinear Ginzburg-Landau equation for Josephson junctions is obtained, from which the precise nontrivial current density and effective potential of the Josephson junctions are found. Based on the resulting potential well, the tunneling probabilities of the associated bound states are computed which are in complete agreement with the reported experimental data. The effects of junction and bias parameters such as thickness of the insulating barrier, cross sectional area, bias current, and magnetic field are fully investigated using a successive perturbation approach. We define and compute figures of merit for achieving optimal operation of phase qubits and measurements of the corresponding states. Particularly, it is found that Josephson junctions with thicker barriers yield better performance in measurements of phase qubits. The variations of characteristic parameters such as life time of the states due to the above considered parameters are also studied and discussed to obtain the appropriate configuration setup.