@Hitch. I suppose I should have visited the link in your signature. I've now remedied this oversight. I should have realised I was dealing with a professional! It's a shame that the author did not use your services, and also a shame that Amazon did not make him! Not worth your professional effort.
However, I gather you are now probably too curious to leave it alone, so I will attempt an answer to your questions to eschwartz.
1. So far as chapter elements are concerned, here are a couple of examples:
Prologue
Spoiler:
<p style="margin:0.00% 0.00% 1.43%; text-indent:3.0em; line-height:150%; "><div style="page-break-after:always"></div><br style="page-break-before:always; clear:both"/></p>
<div style="page-break-after:always"></div><h1 style="margin:0.00% 0.00%; page-break-before:always; line-height:150%; "><span style=" font-size:1.2rem; font-weight:bold">Prologue</span></h1>
<p style="margin:0.00% 0.00%; text-indent:3.0em; line-height:200%; "><span style=" font-size:1.0rem"> </span></p>
Chapter One
Chapter 12
Epilogue
2. Each chapter is in fact shown in the Go To menu. The first entry, as you might expect, is "Beginning". Then page or Location, then Cover. This is followed by an entry for each chapter beginning at the Prologue, going through to the epilogue and even a couple of author links etc listed in the invalid ncx file. The final entry is End.
3. A "grep -i "#?" part0000.xhtml" in the extracted OEPBS Text directory yields no result, but I'm not totally clear on what it is I should be searching for here. A search for just "?" would not be too practical.
regards,
Darryl