Both of the things you raised are now live.
On the risk you flagged. You were right that it existed. Converting to kanji did introduce errors: 「つかれて」became 着かれて instead of 疲れて, 「ないて」became 無いて instead of 泣いて. In plain hiragana neither was possible — the analyser only gets a chance to guess wrong once you give it kanji to choose from.
But please do not feel you asked for something costly. I did read the whole thing, before and after, side by side. I am a native speaker and checking text is close to what I do for a living, so it goes quickly — and eight stories is nothing. Doing this at thirty stories would have been the painful version. You asked at the cheapest possible moment.
I also ran a check rather than trusting my eyes alone: for all 256 lines, generate the reading of the new text and compare it to the reading of the old. Any line where the two differ is a line where something moved. Fifteen came back — 宝物 read as ほうもつ instead of たからもの, 私 as わたくし, 都 as と. It takes about a second, and I will run it every time from now on.
And it cut both ways. One of those fifteen was a mistake that had been sitting there before I touched anything: 守る人 was being read まもるにん, which is simply wrong. Adding kanji is what made it visible. So the change did not only carry risk — it also cleaned something up.
On the spaces. You should not have to print anything and pencil it in. The site already knew where the word boundaries were — that is how tapping a word plays that word. It just was not showing them. Now it can.
There is a third PDF on your storybook page, “word spacing”. The on-screen reader has a switch for it too, off by default.
昔々、 おじいさんと おばあさんが いました。
The kanji helps with the same problem from the other side — 桃太郎 and 二人 break up the line visually in a way that ももたろう and ふたり did not.
Three changes in three days, and all three are yours: romaji made optional, the kanji brought up to normal, and now the spacing. Almost everyone who visits says nothing. The few who say something usually say it is nice. You have told me three times exactly what was wrong, and all three times you were right and I had not seen it.
You wrote earlier that you should have been more careful what you wished for. Please do the opposite.
I would rather say the rest in Japanese. It is written the way you asked for today — with spaces between the words — and at the level of the stories, so I think you can read it.
エマさん、 ほんとうに ありがとうございます。
みっかで みっつ、 このサイトは かわりました。
ぜんぶ エマさんが おしえて くれた ことです。
エマさんは、 はじめて この サイトを たすけて くれた ひとです。
それは わすれません。
これからも、 おしえて ください。
— さざなみ