After a bit of analysis and testing, I have come across the reasons for squeal and vibrations in rotors along with ways to remedy such problems. To start off I will discuss the physics of the brakes...
The holonomic constraint forces between the pad and the rotor induce a perturbation on the lateral flux density of the material which initiates a perpetual resonating motion. The generation of heat seems to facilitate the chaotic interaction forces that intermittently cascade along the rotors' radial axis of symmetry. This is quite peculiar, since the axis normal to the rotors direction of motion creates precession forces and the perturbation should cause the rotor to conform to the calipers' line of motion. Further investigation has shown that the geometry of the caliper indeed has a profound influence on the initiation of the vibrations.
Heating it up changes the rigidity and makes the rotor more susceptible to temporal deformation, thus changing the natural resonating frequency of the rotor/pad interaction. This indicates to me that shimming and facing is in fact a solution to such problems, which should clearly have been implemented in the design originally. However, a caveat of such solutions is that depending on the design, you could worsen the situation, if you do not properly understand where the adjustments need to be made. It just shows that there are too many pot smoking hippies as bike and bike part designers/engineers.
I have nothing against smoking pot, or against hippies, I just don't want them to be designing things. I am concurrently working on building a bike in my machine shop (from scratch). I actually believe that making the brake caliper an integral part of the frame could be the answer to all issues by intercepting the vibrations before they have a chance to be transmitted to the rotor.
I would especially like to thank DT for working with me on many issues, which I would have otherwise discovered the hard way. DT has been tremendously helpful, and has an excellent design himself, which is precisely why I'm using his design as a foundation, but understandably he does not want to try to innovate a new form of integral brake/caliper design, which is an enormous task, and would come with a huge risk of reliability until proven. Since he has helped me so much, perhaps I will return the favor to him some day.
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Thread: Response To Brake Problems