Alright I gave it another try. My interest in fixing this is mostly for technical knowledge at this point, as it's readable with the az3w -> mobi -> epub workaround I mentioned in my initial post.
DNSB: I mended and prettified the HTML with Sigil. Same results. You are correct, Almost everything is in one xhtml. The cover page has its own xhtml, and then the entirety of the book has a different one.
The book is a book of poems, "Cradleland of Parasites" by Sara Tantlinger. The sample on Amazon was, unfortunately, just the table of contents and does not show the error. It first shows up in the first poem. Here's code from the prettified and mended html I have open in Sigil right now:
<div style="page-break-after:always"></div>
<h1 style="margin:1.75% 0.00% 0.88% 4.62%; text-indent:-1.8em; page-break-before:always; page-break-after:avoid; widows:0; orphans:0"><a name="__RefHeading__36330_1247423656"></a><span style=" font-size:1.3rem; font-weight:bold">On a White Horse</span></h1>
<p style="margin:0.00% 0.00%; widows:0; orphans:0"><span style=" font-size:1.0rem"> </span></p>
<p style="margin:0.00% 0.00%; widows:0; orphans:0"><span style=" font-size:1.0rem">I am the rider of the white horse</span></p>
<p style="margin:0.00% 0.00%; widows:0; orphans:0"><span style=" font-size:1.0rem">enigmatic in interpretation</span></p>
<p style="margin:0.00% 0.00%; widows:0; orphans:0"><span style=" font-size:1.0rem"> </span></p>
<p style="margin:0.00% 0.00%; widows:0; orphans:0"><span style=" font-size:1.0rem">I do not ride as the Holy Spirit,</span></p>
<p style="margin:0.00% 0.00%; widows:0; orphans:0"><span style=" font-size:1.0rem">you will find no gospel spread</span></p>
<p style="margin:0.00% 0.00%; widows:0; orphans:0"><span style=" font-size:1.0rem">beneath my horse’s hooves</span></p>
<p style="margin:0.00% 0.00%; widows:0; orphans:0"><span style=" font-size:1.0rem"> </span></p>
The formatting error is:
Rather than the title showing, "On a White Horse", it shows, "a White Horse". Many other poem titles are similarly cut off.
I attempted 2 modifications:
1. Pre-pended a bunch of spaces " On a White Horse" until the title showed fully in Sigil's preview pane. Result: No difference.
2. Pre-pended a bunch of periods "............On a White Horse" and looked in Sigil's preview pane. The periods did successfully move the characters over.
I think I could laboriously prepend periods in front of each mangled title to fix them, but a manual solution like that doesn't seem worth it.
JSWolf: Converting in Calibre was my first try and it reproduced the same issues. But, does Calibre remove in-line styles automatically?