If you want to present objections to the idea that successive changes in the genome can result in the type of evolutionary events that leave you incredulous, then go ahead. If you want specifics on how each metabolic pathway developed or how a given organ was generated, I would like to see how you would propose to study such matters. A lot of the report is speculation. They cannot tell, for sure, that it did develop from trypsinogen. It's just a guess because they're closely related.
Proteins actually tend to end up in a relatively limited number of families.
As far as the genes themselves are concerned, molecular phylogeny does provide some fairly impressive support for evolution in the genes that can be studied. I think that you are trying to set the bar a bit high here. I think that the majority of those actually studying these matters see measurable evolutionary events as rare and noteworhty, but nobody ever said it was supposed to be a rapid or efficient process. Well, except for the Creationists who need to invoke hyper-evolution to explain the diversity of species that have developed since the Flood.