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Adding a bit to what thiago.eec just said, if you've got the ids set in their respective id= lines, as you enter text in the href="" areas, Calibre should pop up a list of the various ids you can use. You ought to be able to cursor down to the one you want and right arrow out of it to select it. If it's not there, then you'll have to type the information. But, copy/paste should make things easier. If the endnotes are not randomly formatted, you might be able to speed things up with a search/replace on their formatting.
Also, and this could just be a matter of a partial copy/paste to the forum, you haven't closed your aside or divs in your 2nd code snippet.
And, I'll also mention that if the book doesn't have too many endnotes and if they're not big honkin' one, I just cut/paste them up to where they're referenced (getting rid of the filename in the hrefs). I even put them directly following the referencing paragraph instead of at the end of the chapter.
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