Over the past few years I have been dabbling with making ebooks. Not too long ago I advised Jisc on how teachers could get started. You may find my assorted posts helpful http://www.zakmensah.co.uk/category/100-things/
I would definitely suggest that getting the workflow right will pay off in the long run, test A LOT and be consistent. For example on a recent project, the writer wasn’t using headings and lists consistently so it took ages to check and recheck. Time that would of been saved if they’d thought about the whole project from the beginning.
If you want to add interactions then this won’t work in all formats/devices so you should have a fallback for that too.
You’ll also be interested in Craig Mod’s ‘post-artifact publishing’. Happy to help in anyway as i really enjoy your blog and its been helpful to me many times.