Amazing news! Does anyone know what percent of pigs spend their in gestation crates? I'm able to find data on overall population numbers, but I can't find what percent of them become pregnant.

I think this is a good article and attacks some assumptions I've thought were problematic. That being said, I think it's worth elaborating on the claim that intelligence scales with moral worth. You say:

 "Furthermore, it certainly is not the case that in humans we tend to associate greater intelligence with greater moral weight. Most people would not think it’s acceptible to dismiss the pains of children or the elderly or cognitively impaired in virtue of them scoring lower on intelligence tests." 

 This seems true, and is worth further discussion. Most famously, Peter Singer has argued in Animal Liberation that intelligence doesn't determine moral worth. It also brings to mind Bentham's quote: "The question is not, Can they reason?, nor Can they talk? but, Can they suffer?" We don't think children have less moral worth due to their decreased intelligence, nor do we think that less intelligent people have less moral worth–so why should we apply this standard to animals? This is why Singer has argued for equal consideration of interests between species. What does this imply, then, about how we should determine the interests of animals?

Perhaps, we may try to count the neurons involved with pain, pleasure, and other emotions–rather than neurons as a whole—and use this as a metric for moral worth. This isn't perfect, it still has many problems, but would probably be better than other approaches. 

To start, I should specify that I haven't read this book, so my comment is based on the passages you've included. 

First of all, this passage discusses the fact that many animals are killed in crop production. While there are some issues in the studies that claim that, I'll set those aside. My issue is that the passage fails to mention that the majority of plants grown on this planet are fed to livestock, and this is an inefficient use of energy, since you lose many calories in the process. For example, 77% of soy grown in the world is used as feed for livestock. Thus, eating factor farmed cow leads to more crop deaths than eating plants. The author does mention grass-fed cows, which make up a tiny proportion of livestock in the developed world. The problem with this is that it isn't scalable. We probably can't feed a country the size of the U.S. on grass-fed cows, hence the existence of factory farms in the first place. It will also be more expensive (more so than plant forms of protein).

Regarding Wolff's health claims, it's harder for me to comment on that since I'm not a registered dietitian. That being said, neither is he. If we ask the largest group of registered dietitians, however, they say that a plant based diet can be acceptable for people at any stage in life.