Awesome post. About the "fantastic two-gene change": can't there ever be a force pushing for a species to obtain two independent mutations more or less simultaneously? What I mean by that is pressure on a species to maintain / promote a few existing mutations in the population (each individual may carry one, or the other, or none, but the offspring of carriers is likely to end up with more than one). I imagine in very narrow bottlenecks this could be the case, e.g. tough ecosystem forcing early humans to a. become bipedal and b. think/plan better. Such bottlenecks could also be caused by inter-species dynamics, climate change, etc.
Actually the more I think about it, the more I am convinced that multiple interacting species introduce a serious argument against the blind hill-climbing view of evolution. Essentially what you have is not a single point on a landscape blindly climbing in the direction of the gradient, but a probability distribution with a given mean point that could jump to another mean currently at its periphery given enough pressure / interference. E.g. a newly migrated predator eating away 90% of variance of the distribution of some existing sheep-like species, leaving only its tough "tail", thus severely relocating the centroid. Maybe this is something trivial I'm just realizing, I'm not a biologist.