Since you seem to have a similar view to me, regarding major project, here's my thoughts...
That similar view is to search out and find the right tools before actually starting the project. I've got some personal ideas that need some kind of document output, so I'm looking at, or at least trying to look at, all the available alternatives to the ubiquitous office suites, which may or may not be the best tools for the job.
First, I've only had time to skim the posts, I may have misread or simply missed something here and there.
Lyx has been mentioned. I just took a quick look at it, and was dismayed to find it has, essentially, zero support for .doc/docx files. And, if memory serves, few export formats if any.
Why, I don't know, just about every other text program I've looked at does.
So it's been removed from my computer... for now. LOL Maybe there is a way to convert it's files, I did not do any searching for something.
Someone mentioned Scrivener. I'm in the process of using the demo, off and on, right now. Even if you don't use this program for the final output, I'd recommend it solely from the aspect of the user's ability to keep all his research notes within your Scrivener project, from PDF files to personal notes to web pages to images. Yes, it will open web pages from within Scrivener, no need to open your browser to view them.
A plus side for you, it would seem, is it directly supports the eBook format. I know nothing about the ebook format, but if that's where you are really going, I'd at least look at this.
At the moment, my biggest personal concern is how it would handle images in the final output. I have not investigated this yet, but need to.
It's not expensive, IMO, $45 US. I do plan on purchasing it simply because the ability to put all my research in the project where it's seems to be extremely easy to access. Even if the final output is done some other way. One advantage of my Mac, the Mac natively produces PDF files, but I don't know how good the output will be.
There are a number of Scrivener tutorials on YouTube, and it comes with a 500+ page manual, all done in Scrivener. Yes, you heard me right, a real live manual in PDF form. And tutorials are built into the program.
Someone mentioned DTP. I.E. a program like Adobe Pagemaker. Which, you obviously don't want to purchase for this.
There is a free DTP program called Scribus, http://www.scribus.net/canvas/Scribus
The Lite version of Calamus is shareware, http://www.calamus.net/calamus/lite.php I used the paid, commercial version on the Atari platform years ago, liked it, but haven't used any DTP software for years.
Serif.com has a reasonably priced DTP program, PagePlus X7, http://www.serif.com/pageplus/
Whether any of these programs do much, if anything, for ebooks I do not know.
And neither will you if you don't check them out.
I had not heard of yWriter, so I'll have to check that out. Have the page in my browser as I write this post.
If/when you settle on something, I wouldn't mind knowing why you picked one over the another. The email address on this post is valid, please use it if you wish.