Certain options may require the PrePub stylesheet. You can also change centering, size, and capitalization of the headers there.
There will be no header at all on passages.
Passage names will not be altered (e.g., to upper case).
Paragraph numbers are arbitrary (though sequential) and are not inserted into links.
Use a numeric entity reference (e.g., §), not a named reference (§).
Provide a path relative to the directory you will be running pandoc in.
The start passage will remain at the beginning.
This should only be necessary if you didn't use a purely Markdown-based story format like Snowman. (Chapbook uses some minor non-Markdown markup.)
It does not convert macros or other scripting.
See the PrePub README or web page for help converting the downloaded file to ePub using Pandoc and PrePub's stylesheet.