And, @Don_Mc : another book that you may find interesting, and somewhat less technical, is Kemp’s The Origin of Higher Taxa. It is not as rich in detail about particular transitions, but if you have a basic familiarity with a variety of major transitions reflected in the fossil record, e.g., mammals from basal amniotes, birds from theropod dinosaurs, tetrapods from lobe-finned fish (which it appears you do not, and MUST have before making the pronouncements you’ve apparently made in your book) it deals with the sort of “process” questions of how one gets from A not only to B, but beyond.
Any assumption that all of this is based upon fallacious reasoning, it seems to me, cannot hold up under much scrutiny. The depth of practical and theoretical work on these topics, from the biochemist who understands it at the smallest level on up to the animal physiologists and paleontologists who understand it at the large-organism level (not to mention such people as ecologists and population geneticists, who understand it at still larger scales), is profound and all-encompassing. I think you will find that the reason people make inferences you wouldn’t is that they are familiar with significant portions of this vast, vast body of evidence.
And this is a mistake people make all the time. People read a couple of books by Dawkins and now they think they truly understand evolutionary theory inside and out, and are well-positioned to critique it. But while some of those books are excellent – no disrespect to them intended – they are FAR from what you need to be an able critic. They are simplified, stripped-down ways of explaining the topic to a general audience; they are not technical works that show you all the detail, nor would they be any good at what they are trying to do if they were.
P.S. To be clear, this problem affects everyone, regardless of point of view. When I took an interest in biology, after having neglected to read much in many years, I felt pretty clear on a lot of things after reading a few Dawkins books. And then I read more, and more, and more, and it became obvious to me that my confidence in the depth of my understanding had been misplaced. I now know much more about biology than I ever have, and am acutely aware of how much greater the knowledge of actual scientists is than my own. A person has to embark on that sort of learning process in order to get a bit past his own particular Dunning-Kruger curve.