Definitely a more challenging question!
If by anthology, you mean a collection of works that fall within a subdomain, and may or may not involve crossovers with other subdomains, may have different pairings, or different kinds of pairings, for example M/F or F/F, and/or may require differing tags per story, then yes, we would permit a Table of Contents in that case. We'd also ask that you tag each story at the top, and disclaim any crossover subdomains as needed in each story.
That was the good news. The bad news is that there is no way to reorder the stories here, since they are posted as chapters within the main story (anthology). In order to change the order, you would need to delete and repost the chapters in the correct order, and if you delete ALL the chapters, you lose the ratings, reviews and hit count data associated with the anthology.
And now for the Bonus Off-Topic Question: Right here in the Writers Corner, you'll see that people have posted all sorts of questions and conundrums. Admittedly, a great many of them seem to devolve into moans about the lack of reviews, but there are some truly useful discussions that crop up from time to time. We also have our Unofficial Guides which really has some gems in there. I suggest that you give us a précis of what you have for Point C and Point E, and see what others come up with as a logical way to bridge the gap. Even if no one hits on the exact Point D, you might find some inspiration in the brainstorming.