Thanks for sharing! One of your questions was about laying out the ebook.

For my own, I started with InDesign but found it too painful to use (I only used it for the cover). I used LaTex (since I had some math equations) but the benefit is that it's all plaintext and easy to modify with quick scripts. It also gives you really nice typography. Again, this is probably most useful if you end up having math equations inside :).