This may come across as a bit odd, and like a lot of work, but I do all of my writing in a WordPress blog. I am producing 2-4 ebooks a month for clients right now, so I needed a system that was efficient in the long run, if work intensive to set up.
I create a new category for each work and subcategories for chapters. I use an exceptionally minimal theme that was simple to modify to use my own css class naming conventions and html tags.
My original workflow required that I view-source and copy/paste the relevant portion into a text editor. The benefit was everything had the correct css classes and html tags already.
Beyond the Manual Workflow
I've since written a plugin that will take an pull all of the subcategories out of a main category and compile it into a single html document and embed my default styles.
- Using WP to write also nets me the benefit of auto version saving so I can always go back and check out where I've been.
- Existing Plugins
- There are also a number of WP plugins that I find extremely useful like language complexity analysis, passive voice checking and some style checkers.
- The immense power of WP's plugin engine means that you can really make it do just about anything you'd like it to.
- I wrote a plugin that essentially does 90% of the manual work for me. I usually end up opening the output file in DreamWeaver and customizing the css a bit before submission to my clients.
- Some of my clients require documents delivered in LaTeX format. I was able to write a plugin that also exports in that format as well.
- Body of Work
- Using WP also allows me to store my entire body of work in my WP database. It is searchable, well indexed and available on anything from my desktop to my telephone.
- This centralization also makes it very easy for me to ensure my work is backed up by a world class technology company.
- Note Taking
- I also use my WP for taking notes on things I am either writing about or thinking about writing about. I find this to be very convenient.
I find the manual method to be more efficient than MS Word. The automation I now have is so much better that I shudder at the thought of losing it.
I just finished reading the link that the OP gave as their process. I basically do the same thing but I use my WP tools to handle most of it. I agree that controlling the html and CSS is the only way to ensure that you are getting what you want.