I looked at this last year and liked it. I ended up sticking with my old setup: using a markdown editing app with leanpub.com for my manuscripts, and Apple Notes to manage research notes.

I think your system is very good, but I decided to stick with my super-simple setup. I have been using emacs for 40 years but use it less now, favoring specialized setups. I mostly use eMacs now for programming with various Lisp languages and I like my Python emacs workflow.