Various forms of misalignment in separated gap waveguides made of periodic bed-of-nails are investigated numerically. Separated gap waveguides which are suitable for wireless power transfer applications are considered in this analysis. Two equivalent problems using perfect magnetic conductor boundaries are derived from the original problem with the periodic structure. The two equivalent problems are validated using simulation and prototype measurements. The equivalent problems are then solved with a parametric sweep to investigate the effect of lateral and rotational misalignment on this type of waveguides. The numerical results are plotted and compared to investigate the tolerance of gap waveguides in terms of power transfer efficiency.