Patrick, thank you for your response.
1. The reason we're using canonical references on those pages is because they are almost identical copies of each other. In the future, we'll create some content on them and they can then stand by themselves.
2. But the original question remains - why is the main page (http://perfectlinens.com/collections/all) missing from the Google index? It's been on the site for a long time, it's one of our most important pages, it's in our sitemap, and robots.txt is not blocking it.
Thank you for your other tips though - I appreciate them, and will put them on our to-do list.