Another update: After I compiled via KindleGen, the samples provided by Doitsu didn't work, but my old code, i.e.
body:
<span class="endnote-reference1"><a href="part0037.html#en3" id="enref3" type="noteref">3</a></span>
endnotes page:
<p class="endnote-text" type="rearnote"><a href="part0004.html#enref3" id="en3"><sup class="calibre70">3</sup></a>
HAS STARTED WORKING!! Yahoo! Apparently, all I needed to do was compile via KindleGen. Somehow the Calibre AZW3 conversion was the problem.