Affirmatives

応 is listed under "Synonyms" in the entry for はい. I'm a little skeptical of your etymology for 然り. Where did you get it?

Re: 応, such use of the kanji would likely have been ateji for native OJP-derived おお (ō). The only usage I can find of it is in the set phrases 否も応もない (ina mo ō mo nai) or 否でも応でも (ina de mo ō de mo), both essentially meaning "whether one disagrees or agrees", i.e. "to have no choice".

Re: 然り (shikari):

（副詞「しか」にラ変動詞「あり」の付いた「しかあり」の変化）

Shōgaku Tosho (1988) 国語大辞典（新装版） [Unabridged Dictionary of Japanese (Revised Edition)] (in Japanese), Tōkyō: Shogakukan, →ISBN

〔「しかあり」の転〕

Matsumura, Akira, editor (2006), 大辞林 (in Japanese), Third edition, Tōkyō: Sanseidō, →ISBN

《副詞「しか」にラ変動詞「あり」の付いた「しかあり」の音変化》

Matsumura, Akira (1995) 大辞泉 (in Japanese), First edition, Tōkyō: Shogakukan, →ISBN

Ok. I was under the impression that the original kanji 応 as borrowed carried a meaning of "agree", though.

Yeah, it's a bit fuzzy. Shogakukan's entry defs in JA say basically that it means primarily "reply, respond", but with a meaning of "agree" in there too for the set phase 否も応もない (ina mo ō mo nai); Daijirin's entry lists 承知 (shōchi, “know; understand; consent or agree to something; permit, allow”) as a synonym. It's also used in 呼応 (koō, “call, hail; agree with (as in grammatical agreement); in cooperation, in concert”).

Hearkening back to your initial question about affirmatives, I think Japanese はい (hai), うん, and おお (ō) come closest to meaning plain-old "yes", with the caveat that they also mean other things depending on the context. Then again, Shogakukan's pretty good about including the oldest quote for first usage, and I don't see the Kojiki or Man'yōshū listed (and I'm not familiar with most of the more-recent titles shown, but quick checks suggest they're from kabuki plays or other monogatari), so these might not be old enough to meet your criteria.

Does that help?

Yeah, I think I have a better understanding now. So, in terms of etymology, I would guess that うん and おお developed out of onomatopoeia. Do you have any more insight about the etymology of はい?

I don't have much. The Kokugo Dai Jiten quotes for early usage don't date any further back than the late 1700s, while Daijirin doesn't give usage quotes, just usexes; same for Daijisen. None gives any etym.

The etym in the JA WT entry at ja:はい suggests a borrowing either from Cantonese 係／系 (hai6, “yes; it is, there is”) or from Mandarin 拝 (bài, “to kowtow; to worship; to salute; to pay respect”). The Cantonese term could be viewed as similar to other languages' versions of "it is so," while the Mandarin term could be seen perhaps as "I acquiesce, I go along with what you say."

I'm intrigued by how late this borrowing might be, judging from the late date of quotes in the KDJ, and I wonder at how that might have happened -- perhaps something in the popular media helped spread the term? No real idea.