Previous studies by Haq, Webb and others have demonstrated the design of aperiodic waveguide structures to act as filters and mode converters. These aperiodic structures have been shown to yield high efficiency mode conversion or filtering in lengths considerably shorter than structures using gradual transitions and periodic perturbations. The design method developed by Haq and others has used mode-matching models for the irregular, stepped waveguides coupled with computer optimization to achieve the design goal using a Matlab optimization routine. Similar designs are described here, using a mode matching code written in Fortran and with optimization accomplished with the downhill simplex method with simulated annealing using an algorithm from the book Numerical Recipes in Fortran. Where Haq et al. looked mainly for waveguide shapes with relatively wide cavities, we have sought lower profile designs. It is found that lower profiles can meet the design goals and result in a structure with lower Q. In any case, there appear to be very many possible configurations for a given mode conversion goal, to the point that it is unlikely to find the same design twice. Tolerance analysis was carried out for the designs to show edge sensitivity and Monte Carlo degradation rate. The mode matching code and mode conversion designs were validated by comparison with FDTD solutions for the discontinuous waveguides.