Hi there
I saw that there wasn’t yet a response to your post. I am a brand-new Scriveneer too (and this my first post ever), so can’t offer much yet by way of advice. However, I’m in a similar position of having written an MA and PHD in Word, but am now turning to Scriv to write my first book (I’m in humanities). And am loving it. The binder (I have a folder per chapter, with individual docs representing paragraphs or sections, and an ever growing Research folder) really allows me to think and write creatively, rather than along strictly linear lines. Screen splits are a blessing when transcribing or copying materials out.
Word targets (cmd-shift-T) help me stay on track and are good for satisfaction at the end of the writing day (providing you are actually writing, of course…). Outliner view I’ve set up so that I can see my completion due date, target no. of words, and a column which shows actual word count, so I can keep a keen eye on my progress.
I am still struggling with referencing, which you will need to think about carefully and plan thoroughly. For my PhD I still wrote out footnotes by hand. Bad idea! I now keep a Zotero database and would LOVE for a connection between Scrivener and Zotero but understand from posts elsewhere that this is not possible. So I drag short-hand refs into the main text, and when it comes to exporting my Scriv book into a word processor, I’ll then have to either RTF-scan the lot, or reinsert the refs by hand (a few days work at least). Still I decided that the beauty of Scrivener would reward me enough and that I would worry about the refs later (whilst keeping absolutely meticulous details of where I get my quotes from, and whilst entering each new book, article, etc. into Zotero as I go along).
Not sure what you mean by ‘publishing’ your dissertation. Scrivener has so many ways of outputting your text, and only publisher-specific style guides will tell you what you need. At the very least, your material will always live in Scrivener and look like you want it to look, and you are never more than a few steps away from a customised export of your writing, which is great.
Anyway, the reason I really made the leap to Scrivener was this awesome review http://chronicle.com/blogs/profhacker/scrivener-scrivening-scriverastic/23026, which spells out how to use Scrivener for a large academic research project, but also, for instance, designing a teaching module. All in all, a good tool for the academic! Good luck with your PhD!