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This answer got me wondering how relevant the presentation in 万葉仮名 is to finding a 漢字 for a given word.

As far as I understand, 万葉仮名 are used largely for phonetic value. Knowing that some word was written with some combination of 万葉仮名 would only carry any significance if words were written consistently with the same characters. Do texts in 万葉仮名 indeed choose 万葉仮名 consistently or is a lot of the choice a stylistic choice on part of the author?

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Not an answer per se, but Nitobe seems to have used a set of different characters for これ、それ、あれ (meaning multiple ones for each -- he's consistent in referring to the same for the same referent) – virmaior Apr 8 '14 at 1:17
I know Marc Miyake's 'Old Japanese: A Phonetic Reconstruction' has a discussion of this, though I don't remember the details. I do remember that he sees some definite patterns in man'yougana choices over time. – Sjiveru Apr 8 '14 at 15:48

According to Wikipedia, it would appear that there were in fact a wide range of characters used for any given sound prior to the de-facto standardization that was the creation of the Kana syllabaries (keeping in mind, of course, that at their roots the kana characters are either cursive forms of characters [ひらがな] or isolated elements of characters [カタカナ]).

That said, it's interesting to note that from a historical perspective the system pretty clearly differentiates between two versions of the vowels i, e, and o for most columns. So in that regard there was some consistency, but other than that it really was a matter of stylistic preference.

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