My information is from similar sources as yours, as well as reading done on my own while in college. The specific studies and researchers I remember I will give names for - I unfortunately do not recall all of them and my brain certainly does not create a proper Resources & References file for everything I learn throughout my life.
Mammalian-focused biologists in this area typically know a lot about coyotes since they are so prevalent here so there's a lot to talk about with them. More recently, wolves have started making their way back north, so it's a hot topic of research these days too.
The studies that are done actually comparing wolf and coyote diets and digestion are largely done through scat analysis since such invasive research methods as going out to kill samples and dissecting their bodies aren't really looked upon with favour. Back before people were so touchy about it, Gipson in 1974 did a really great study by examining coyote guts to look at their digestion and focused on seasonal variance, basically showing the great adaptability of their digestive system by the change in diet they endure during different seasons. His study was focused on one area but there were other studies conducted later focusing on the coyote's ability to also adapt based on their geographical location. Obviously coyotes in the Midwest are going to nibble their way through a corn field far more often than coyotes living in deserts out west. I will note here that Gipson's studies of course do not mean that coyotes are as efficient at digesting plant matter as a herbivore - it simply means that coyotes eat a lot of plant matter because it's available (and probably, particularly in cases of fruits, because they like it.) Oh, they also eat insects - that was the third most common food source Gipson found.
Otherwise the comparison is simply looking at each individual animal's unique characteristics and noting things that one has that another does not have.
David Mech did a number of wonderful studies on wolves, but unfortunately most of the studies on wolf digestion are not actually wolf digestion studies but dog digestion studies that he takes a lot of information from to apply to the wolf. However if you read his studies he himself says that dogs likely lack a lot of the enzymatic power of a wolf - basically, that a wolf has things that dogs no longer have because they didn't need them. I believe it was also Mech that found that wolves have much stronger stomach acid than the domestic dog. He also talks a lot about the feast-or-fast existence of a wolf and how their eating habits are intended to essentially gorge themselves to prepare for going without food for a long amount of time.
The studies Mech used to learn about wolf digestion discussed the great adaptability of a dog's digestive system - something that coyotes quite clearly have. He believes a wolf could have this ability as well, but it's not something that was studied. This is not spontaneous evolution of the pancreas, it's simply a function of it. It was not Mech's study (he just talked about it), but this ability of a dog's pancreas is scientifically documented. I think it was a study in the 1980's. This may or may not have been the studies that involved injecting deer protein (?? don't recall exactly what is was from a deer) into a dog's stomach to see what happened... can't remember the specifics of that study.
So given everything here, there's a few main points. First, coyotes and dogs eat pretty much whatever given the chance. A wolf, on the other hand, will gorge itself on a meal and will also cache food (something the coyote does not do, but some dogs will do) to store it for later consumption. Wolves will eat berries, but they do not turn to feasting on whatever they can find the way coyotes and dogs do - instead, they will simply fast... and their bodies allow for this in a remarkable way.
Mech has found that the wolf has such an incredibly efficient stomach for digesting meat. Dogs and coyotes do too; however, dogs and coyotes will also feast on other things whereas a wolf will not turn it's typical gorging eating behaviours on fruits. Why not? Mech's presumption is that a wolf is MORE efficient at digesting meat than a dog is, so perhaps the wolf is not quite as adaptable as a coyote and a dog are. The wolf machine does one thing incredibly well; the dog and coyote machine do that slightly less well but also do something else slightly better, too. If a dog and a coyote gain little nutritional benefit from fruits and vegetables yet still eat it anyway, a wolf must gain even less - or nothing at all - from fruits and vegetables. There is no scientific sense to a wolf eating something that does it no good; however there is also no scientific sense to a coyote eating something that does it no good, yet we know coyotes eat these things and therefore it must do them SOME good.
So that's where you get the conclusion that a dog and a coyote are more similar in their eating behaviours and digestive systems than a wolf and a dog. They do it, therefore there's a reason. Exactly what that reason is, I do not know, and I'm not sure we will know unless invasive research is done. Somebody else can write for a grant from the government to determine the why and once they do, we can reevaluate, but right now that's the conclusion that has been drawn among a lot of the biologists I have talked to given the information we know right now (and it makes sense to me, so I agree with it pending more research.)
That is speculation also. No one can say for certain what they ate over a long period of time. ... Did the pancreas suddenly start secreting enzymes to digest plant material? How did it do that?[\quote]
Of course it is speculation, of course no one can say for certain what the coyote ate many years ago. However, it is also speculation that dogs evolved from wolves. Genetic similarity is not proof of evolution - even Francis Collins will tell you that. I notice you are not so quick to point out that it is ultimately speculation that dogs have evolved from wolves - perhaps because it does not suit your argument to point that fact out?
Evolution is truly ALL speculation, including within humans, as we do not have primitive cavemen bodies to dissect and compare with our modern ones.
Finally, if I - or you, for that matter - could answer HOW bodies evolve, I suspect you would not be on the internet arguing on a dog forum. I, for one, would be incredibly loaded, and likely deeply entrenched in scientific work - or perhaps playing on a beach in Hawaii doing jack all for the rest of my life. Either or.
Anyway, I hope that answers your questions.