His IDs are unique. However, if you are going outside the current file, you have to include the filename. Looking at your sample, I added back1a and back3a for the back links.
Code:
<a href="endnotes.xhtml#massa" epub:type="footnote" id="back1a">[1]</a>
<p><a id="massa" epub:type="endnote" href="Section0001.xhtml#back1a">[1]</a><span class="endnote"> Shiny footnote text here.</span></p>
You will need to add the epub:type and aside directives as needed.