Thought I'd share the command-line options I used to generate a proper table of contents from a mix of feeds downloaded using feeds2disk. I first made sure the root index.html had proper links to each of the feeds' sub-directories' index.html files. Then I ran the following command on the root index.html file:
html2epub index.html --level1-toc=//*[@class="feed"] --level2-toc=//*[@class="article"]
Thanks for pointing me in the right direction, Kovid! Maybe this will help someone else, too.