I can't share a one size fits all tool for making ebooks, but earlier today a new validation tool which should be able to tell you why your ebook failed to pass muster at each of the major ebookstores. It's called FlightDeck, and it is being launched today by eBook Architects.
This tool goes beyond existing validation tools in that it not only identifies errors in Epub and Epub3 files, but it also promises to tell you whether each retailer will accept the file.
Run your ebook through the FlightDeck website and it will spit out a unique "Retailer Acceptance Grid" which will tell you whether your Epub file will be accusers whether their EPUB files will be accepted by eBook partners including Amazon, Apple, Google, B&N/Microsoft, Kobo, and Net Galley. This checklist was developed with direct input from the ebook retailers and includes the same validation checks the retailers run when you upload a file to their servers.
And in addition to validation, FlightDeck also enables users to edit the title, author, and other metadata in their Epub files.
FlightDeck is going to be in beta for the next couple months so that users can provide feedback and help eBook Architects make plans for future enhancements and additions.