Vocab Builder should be available (but I don't care about it plus my Kindle Touch doesn't support it, so I can't say from experience). And X-Ray Builder seems fairly reliable if you invest a bit of time in it.
re: typography, EPUB and AZW3 support fonts embedded inside the ebook file, just like DOCX and PDF do. calibre has a Polish Book tool which can auto-embed fonts for you.
As for spacing etc., some people complain about kerning and (lack of) hyphenation, but no words will run together, and bad line breaks are an artifact of a badly coded ebook file (so complain to the publisher for not proofing it). Supposedly the lack of hyphenation results in occasional badly-spaced words on justified text, not that I have noticed, but I have seen that complaint once or twice...
Do not worry about jailbreaking, Amazon doesn't typically check for signs of a jailbreak on warranty returns. It would cost too much.
And the jailbreak stays out of the way of firmware updates.