I’ve only read your point number 1 so far but it occurs to me that a) where are the ‘thousands upon thousands of transitional missing links? and b) for any ‘good’ mutation to have a true and lasting effect on a large population then the majority of the population would have to acquire the same beneficial mutations in BOTH the male and the female [as well as the MAJORITY population]- sorta kinda like obvious here why mathematicians [not creationists] are the largest majority group to overwhelmingly reject [macro-]evolution. The math simply does not support it and neither does the fossil record - you need much much more than billions of years. Even trillions won’t do!
Oh and it is also quite convenient that ‘beneficial’ mutations always get lumped in with natural selection in most of the evo arguments. IOW Motoo Kimura has to hypothesize much more than he proves -so Sanford and Kimura simply share a difference of opinion and bias. Also note-worthy that Sanford was at one time completely sold on atheism and evolution, so at least he has fully explored both sides of the argument [something I highly doubt for Kimura and other highly researched [one-sided] evos.
But just for laughs I’ll keep reading and responding as time allows...
Regarding transitional species, by the very definition of the term, these are a change from one species to another, over time. In other words, their occurrence, by the nature of the change, is fewer than the occurrence of the stable species from which it arose, and the stable species to which it settles. Since fossils themselves are rare, it would be logical to expect transitional fossils to be even rarer. However, this does not imply that they didn't exist. One of the biggest finds affirming this was the recent findings of the Pakicetidae fossils. Pakicetidae are the ancestors of modern whales.
http://en.wikipedia.org/wiki/Pakicetid

