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As another person working on a Masters degree I understand the foot noting expectations, my last paper was only like 20-30 pages, but had over 100 footnotes!
My recommendation in ebook land is to just use endnotes instead. Linked or not will depend on the reader and the software you use. I would try my best to get them linked, and see if you can get the linking working on Nook and Kindle, but beyond that let it go. So long as the notes are there you are covered.
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