Over the past couple days, I discovered a simple, direct method for calculating frequency responses with a combination of COMSOL and any plotter such as Excel or MatLab. The simple case of rectangular prism of steel was analyzed using this method; details will be posted shortly on the COMSOL Wiki page. The frequency response matched theoretical reasoning: the bar acts as a simple mechanical low-pass filter, rapidly attenuating driving frequencies at the base beyond the first eigenmode.
It therefore shouldn't be too difficult to extend this analysis to the MC1/MC3 stack. The many eigenfrequencies will produce a more complicated transfer function, and so more data points will be taken.
The major shortcoming of this method involves dealing with the imaginary components of the eigenfrequencies. As of now, I haven't found a way of measuring the phase lag between the drive and the response. I also haven't found a way of changing the damping constants and therefore playing with phase components.