Hi, I know this is an old thread but I had the same issues with converting to vertical text for kindle. I have a little bash script that works in two stages to produce a AZW3 file that works on my kindle paper white. It's for converting the XHTML files you can get from aozora.gr.jp, but it could easily be adapted for other sources by adjusting the two lines that call ebook-convert. Here it is:
Code:
name=${1%%.html}
ebook-convert "$name".html "$name"
echo -en "\n\
body {\n\
\t writing-mode: vertical-rl;\n\
\t line-break: normal;\n\
\t -epub-writing-mode: vertical-rl;\n\
\t -webkit-writing-mode: vertical-rl;\n\
\t -epub-line-break: normal;\n\
\t -webkit-line-break: normal;\n\
\t line-height: 150%;\n\
\t padding: 1em 1em;\n\
\t font-family: serif, sans-serif\n\
}\n"\
>>"$name"/page_styles.css
sed -i -e 's:</metadata>:<meta\ name="primary-writing-mode"\ content="vertical-rl"/>\n</metadata>:' "$name"/content.opf
sed -i -e 's:<spine.*:<spine\ toc="ncx"\ page-progression-direction="rtl">:' "$name"/content.opf
sed -i -e 's/<dc:language>.*/<dc:language>jpn<\/dc:language>/' "$name"/content.opf
zip "$name".zip add -j "$name"/*
ebook-convert "$name".zip "$name".azw3
rm -Rf "$name"
rm -f "$name".zip