Did you need to embed fonts for some reason? Are you using special fonts that are required for proper display of your text? I never embed fonts unless absolutely necessary (and frankly it never has been so far in my short ebook design career) but I understand that if you do, it's best to use free fonts such as Google Fonts for this purpose. If not embedding fonts is what you intended, then make sure "Include Embeddable Fonts" is unchecked in the Advanced tab of the epub export dialog box.
DiapDealer, Book Proofer is a Mac application available through iTunes Connect that allows a user to easily sync a book to their iOS device without going through iTunes for the purpose of proofing. It solves a problem with iTunes that makes it hard to sync a new version of the same book if the metadata is identical.