The most significant misunderstanding Johnson repeatedly exhibits is that he thinks modern evolutionary biology is synonymous with his understanding of the meaning of the term "Darwinism": all biological change is due to mutation and natural selection. The fact that other mechanisms, such as genetic drift and endosymbiosis, are now an essential part of the picture, seems to have escaped him completely. Ignorance or dishonesty? I'm not sure; maybe it's a mixture of both.
"The fossil record hasn't gotten any better, in the intervening century and a third... [since 1859]"
Another blatant lie. Archaeopteryx was discovered in 1861. Since then, we have thousands and thousands more discoveries that add significantly to our understanding of evolutionary history: Diplodocus, Maiasaura, Paranthropus, Australopithecus, Ardipithecus, Pakicetus, just to name a few.
These examples, chosen just from the first 22 minutes of the video, give the flavor of the ignorance and misrepresentation offered up by Johnson. This video would make a great educational experience and expose the dishonest anti-intellectualism at the heart of creationism.