Ok, so, I used League Gothic Regular and it was stripped. You indicated that's a go-to font for you, so we're pretty sure that it SHOULD work. So there seems to be some issue that is not the fonts. (Though again, on League Gothic Regular as it did on Condensed, Kindle Previewer kicks out a warning saying it is a Type-1 font. But it's not a fatal error, and the resultant mobi has the font intact. It's not until upload that it is stripped.)
In a past life I used to hack (not code, just monkey with extant pieces to make them do something new) C and I've lost track of the number of times I hunted down a single piece of punctuation. The weird thing is that you would expect it to fail in Previewer if it was going to fail. Makes you wonder what exactly Amazon is doing on their servers... *sigh*
As far as conversion, everything I have tried works just fine except upload to KDP. I can convert via Previewer (which AFAIK is the equivalent of naked KindleGen, just with a GUI) or Calibre and end up with a file that looks perfect. All files included that should be. It is only when I get to the step of pulling the file back down from KDP that the fonts have magically disappeared.
For the fun, here's my .opf (with just League Gothic included):
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
<package xmlns="http://www.idpf.org/2007/opf" unique-identifier="BookId" version="2.0">
<metadata xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns
pf="http://www.idpf.org/2007/opf">
<dc:identifier id="BookId" opf:scheme="UUID">urn:uuid:f3875132-d23d-4451-b435-4f0a28162caa</dc:identifier>
<dc:title>Day Breaks</dc:title>
<dc:creator opf:file-as="modification" opf:role="aut">Mathew Reuther</dc:creator>
<dc:language>en</dc:language>
<dc:contributor opf:role="aut">Mathew Reuther</dc:contributor>
<dc
ublisher>Oakenbrand Press</dc
ublisher>
<dc:date opf:event="publication">2013-01-11</dc:date>
<dc:contributor opf:role="cov">Bridgette Reuther</dc:contributor>
<dc:contributor opf:role="tyg">Mathew Reuther</dc:contributor>
<dc:format>application/x-mobipocket-ebook</dc:format>
<dc:language>en</dc:language>
<dc:date opf:event="creation">2013-01-10</dc:date>
<dc:date opf:event="modification">2013-07-19</dc:date>
<dc:contributor opf:role="ill">Bridgette Reuther</dc:contributor>
<meta content="0.7.2" name="Sigil version" />
<meta name="cover" content="Cover.jpg" />
</metadata>
<manifest>
<item href="toc.ncx" id="ncx" media-type="application/x-dtbncx+xml" />
<item href="Styles/core-styles.css" id="core-styles.css" media-type="text/css" />
<item href="Text/TitlePage.xhtml" id="TitlePage.xhtml" media-type="application/xhtml+xml" />
<item href="Text/QuickMenu.xhtml" id="QuickMenu.xhtml" media-type="application/xhtml+xml" />
<item href="Text/Dedication.xhtml" id="Dedication.xhtml" media-type="application/xhtml+xml" />
<item href="Text/Contents.xhtml" id="Contents.xhtml" media-type="application/xhtml+xml" />
<item href="Text/Afterword.xhtml" id="Afterword.xhtml" media-type="application/xhtml+xml" />
<item href="Text/Bio.xhtml" id="Bio.xhtml" media-type="application/xhtml+xml" />
<item href="Text/Copyright.xhtml" id="Copyright.xhtml" media-type="application/xhtml+xml" />
<item href="Text/Description.xhtml" id="Description.xhtml" media-type="application/xhtml+xml" />
<item href="Text/Return.xhtml" id="Return.xhtml" media-type="application/xhtml+xml" />
<item href="Text/Works.xhtml" id="Works.xhtml" media-type="application/xhtml+xml" />
<item href="Images/imprint.jpg" id="imprint.jpg" media-type="image/jpeg" />
<item href="Text/Fonts.xhtml" id="Fonts.xhtml" media-type="application/xhtml+xml" />
<item href="Images/scenebreak.jpg" id="scenebreak.jpg" media-type="image/jpeg" />
<item href="Text/DBChapter1.xhtml" id="DBChapter1.xhtml" media-type="application/xhtml+xml" />
<item href="Text/DBChapter2.xhtml" id="DBChapter2.xhtml" media-type="application/xhtml+xml" />
<item href="Text/DBChapter3.xhtml" id="DBChapter3.xhtml" media-type="application/xhtml+xml" />
<item href="Text/DBChapter4.xhtml" id="DBChapter4.xhtml" media-type="application/xhtml+xml" />
<item href="Text/DBChapter5.xhtml" id="DBChapter5.xhtml" media-type="application/xhtml+xml" />
<item href="Text/DBChapter6.xhtml" id="DBChapter6.xhtml" media-type="application/xhtml+xml" />
<item href="Text/DBChapter7.xhtml" id="DBChapter7.xhtml" media-type="application/xhtml+xml" />
<item href="Text/DayBreaks.xhtml" id="DayBreaks.xhtml" media-type="application/xhtml+xml" />
<item href="Text/PredawnRescue.xhtml" id="PredawnRescue.xhtml" media-type="application/xhtml+xml" />
<item href="Text/Prologue.xhtml" id="Prologue.xhtml" media-type="application/xhtml+xml" />
<item href="Images/Cover.jpg" id="Cover.jpg" media-type="image/jpeg" />
<item href="Fonts/LeagueGothic-Regular.otf" id="LeagueGothic-Regular.otf" media-type="application/vnd.ms-opentype" />
</manifest>
<spine toc="ncx">
<itemref idref="Description.xhtml" />
<itemref idref="TitlePage.xhtml" />
<itemref idref="Works.xhtml" />
<itemref idref="Fonts.xhtml" />
<itemref idref="QuickMenu.xhtml" />
<itemref idref="Dedication.xhtml" />
<itemref idref="PredawnRescue.xhtml" />
<itemref idref="Prologue.xhtml" />
<itemref idref="DayBreaks.xhtml" />
<itemref idref="DBChapter1.xhtml" />
<itemref idref="DBChapter2.xhtml" />
<itemref idref="DBChapter3.xhtml" />
<itemref idref="DBChapter4.xhtml" />
<itemref idref="DBChapter5.xhtml" />
<itemref idref="DBChapter6.xhtml" />
<itemref idref="DBChapter7.xhtml" />
<itemref idref="Return.xhtml" />
<itemref idref="Afterword.xhtml" />
<itemref idref="Bio.xhtml" />
<itemref idref="Contents.xhtml" />
<itemref idref="Copyright.xhtml" />
</spine>
<guide>
<reference href="Text/Contents.xhtml" title="Table Of Contents" type="toc" />
<reference href="Text/Description.xhtml" title="Start" type="text" />
</guide>
</package>