Somewhat belatedly, from the research I did for the blog post you mention, this is what I understand the sequence of events to be:
Song is written in Yiddish, fails to gain mainstream popularity even when the songwriter produces an English version, sinks into obscurity.
Teddi Schwartz and Arthur Kevess dig it up in the 1950s and translate it into English; ...
From an internet search for dona dona japanese translation, which I ran after it occurred to me that there might be a quick answer out there, I found this blog that mentioned a 1966 translation by Yasui Kazumi. An MIT's Jewish A Capella site also gives the same translator.
Just to further double-check things, I ended up on the Japanese Wikipedia page for ...
Yes, it is a stopwatch. Ikuhara Kunihiko (Director/Producer, Storyboards, Original Concept) answered this question in an Animage interview with Be-Papas, the animation studio that created Utena:
Translation by a fan:
Animage magazine: The next question came up most often.
Question: What does Miki measure with his stopwatch? (reader from Hokkaido)
The progression from butterfly to leaf suggests grasping at the "fundamentals" of something: the butterfly started from a catepillar eating a leaf. However, this idea of progressively digging deeper does not really explain the monologue progression. For instance, with Shiori, the progression is from:
Always hated Juri and wanted to take something ...
I don't think so. Lyrics from Utena duel songs talk about high abstract concepts which do not have a direct significance to the duel they accompany (or any other duel). In my opinion, it is just inicidental.
tl;dr: Utena probably wins because of some sort of spiritual or moral quality she has.
Why is Utena able to win?
In Utena's second duel, Utena is losing until she "absorbs" power from the prince. Moreover, Touga, who is watching the duel, says:
What was that just now?! Was that the power to bring the world revolution? The Power of Dios?!
Touga's explanation in the manga
In the third volume of the manga, before their second duel together, Utena asks Touga:
Why do you want it so much? "The power to revolutionize the world" … I've never understood it.
Touga's response to this is:
Oh. That's easy. Tenjou, have you ever felt that you were an outsider? That this place we look down ...
As Gorchestopher H has said
here is also an element of coming-of-age. She becomes involved because her time has come
this is correct as being one of the reason however,
Utena becomes involved because of the way the Rose Bride was being treated
This is half-true. Yes Utena protects Anthy but this is because of Utena's role as the "prince" that ...
That episode was . . . weird, as weird as when Nanami became a cow.
Anyway, my interpretation of it was based on the fact that the episode "Nanami's Egg" falls into the Akio Ohtori Saga. This is roughly two thirds of the Apocalypse Saga. The content is more sexually suggestive in this saga: scenes involving Akio's car seemed to always be sexually suggestive,...