I've released a new version that contains mostly bug fixes to CSS Cleanup, as well as the ability to normalize em/en dashes.
I've also been thinking about adding another tool that could inspect the book content and show the user the suspect issues without doing anything about them, so the user can analyze the book and see what kinds of issues there may be and inspect them manually before using the other tools, or manually fix them. Categories would include things like suspect quotes, dialog split into different <p> elements, PDF/TXT conversion artefacts like lines split into different <p> elements, possible hyphenation remants like <word><hyphen><space> in the middle of the line, invisible control characters like soft hyphens or word joiners, etc.
I would probably do it for myself regardless, but I'd be interested in knowing if anyone else had use for an inspection tool, and if there are any recurring issues when working with ebooks that it could detect that is not already covered by the other tools.