I think that Jim Behnke's and Paul Nelson's posts covered most of the details about where the numbers originated and what they compare. I think it's pretty clear now that a lot of morphological change in animals would be expected to be regulatory in nature. We know from biochemistry that organisms share a high degree of common processes and that these similarities increase as more closely related organisms or compared. I am aware that many diseases can be attributed to rearrangements. For example, we often only look for differences when we see a problem.
Asymptomatic variation tends to receive less examination.
I've just bounced this question off a biosystematics friend of mine and she can't think of many large, systematic surveys in humans to investigate it. I don't know how the possibilities of surviving the specific events that lead to humans could be determined today. Perhaps one could look it up the new archives. Sequence comparisons are not the end-all of evolutionary phylogeny. Some things, such as the timing and propagation of regulatory signals and how they relate to overall morphology are probably decades from being understood.