'So I guess I will move them all to the end.'
With short footnotes the hover effect of a link could be an alternative too.
Example: <a href="endnotes.html#123" title="This is exactly the text as in the foot-/endnote.">
When moving with the mouse on the link the text of 'title' is shown like a tooltip.
I have checked it with the Calibre viewer and it works fine in epub.
I've also made a conversion html --> prc with Mobipocket Creator.
The text of 'title' wasn't shown by the Mobipocket emulator but it was shown correctly on the
Calibre viewer again.
Otherwise: When I used Calibre for the conversion prc --> mobi or the original html --> mobi,
the text wasn't shown. So how is it with kindle?
I don't know if it is worth the work only for epub, but the reader hasn't to jump forth and back for endnotes.
And additional all endnotes are compiled in the file 'endnotes.html'.