what do three-quarter chapters taste like?

I would always opt for the htmlling version. of course it is quite a bit of work. but you could upload the endnotes in bulk to the biblio and use the bib tag, similar to fn it creates a footnote with link to the biblio database. I can help if help needed.
you could start posting it as a standard research journal entry and later, by using the 'outline' function, in the edit menu (on of the tabs on top) integrate it into a 'book' in drupal language.
with a book you can create subheadings which get translated into clickable table of content, such as I did here http://www.thenextlayer.org/45RPM

a book can also be exported in printer friendly format
if help is needed, I am here looking at a long bank holiday weekend. maybe i go to the park and do some reading there but mostly I will be here, doing research and writing myself

both Ranciere and Badiou seem to have quite a bit of currency in art theory, by which i mean social, political, philosophical writing that is relevant for art, not necessarily about art. this website is also quite good regarding the content, not the design http://www.after1968.org/index.php/texts/view/8

Dearest

as much as I agree that it is a sign of good character to be humble and not overstate one's achievements, it is also not good to move into the opposite direction too far and always talk oneself down. The first paragraph already is so good that when reading it I first thought it is a quote from some famous research theorist like Focault or Ranciere or Badiou;-)
No, seriously, this is a quoteworthy passage:

The process of research feels like navigating a vast river by executing a series of hops and leaps across those stepping stones which draw your attention. At a certain point you realise that the path you are taking along the currents of ideas and potentialities is leading somewhere in particular, even if you did not know this at the outset. From the infinite set of possibilities offered by the river you have semi-intuitively selected one course, and your focus sharpens. There might be regret for the journeys now not pursued, but also pleasure in finally understanding where you are heading.

Also, you were right to advise us to "have a look at it". The way you designed the table of contents is very instructive, a good way to organise one's work, an example to follow or draw conclusions from. Then throughout the writing is very good and informative and mostly dense, economic in a positive sense. Thus, I learned already a lot about asian citizen journalism. There are just occasionally sentences which do not quite fully work such as this one

Hong Kong In-Media is a paradigm of a heterogeneous mode of contemporary cultural activism

that something can be a paradigm of a heterogenous mode is maybe difficult to get, because what is a paradigm, isnt it a heterogenous mode? or is it homogenous? Or maybe you want to say that it is part of the paradigm of contemporary cultural activism and the heterogenous through me off course? I am sure you will spot such things in any further rewrites anyway.

another small point is the following:

"Whereas mainstream corporatised media exists to return a profit for shareholders (mainly through sale of advertising 'real estate'),"

I would be slightly careful with such strong assertions. while it is true that corporate media exist to create profit for shareholders, most of them, if we are talking of the press for instance, are still fulfilling some of the functions that make it the fourth estate, that is, providing checks and balances for parliamentary democracy, for example. that they have frakked it up and mainly seem to be there to be selling ads is another story, yet a free press is guaranteed by constitution in most liberal democracies, it is a constituent part of the system. Sometimes I also make the same mistake that my writing sympathises too strongly with the subject covered, especially if it is an activist cause.

But overall the writing as such and the thesis too is all very advanced. I'm envious. Sometimes when we are working on something big we feel we are always still at the bottom of that hill or only halfway through, yet sometimes actually we have already reached the end of the upward struggle and there is enough there that now it takes on a dynamic of its own. I think you have reached that point. This work needs probably mostly some more polishing and some crucial final clearings. because you have so meticulously listed the word count, I can say think you are right, you should cut the sub-chapters down to the aim length, - cutting it by the current proportion between what you have and what you aim it should benefit the work, which is something I say from a very general excperience and not specifically about your thesis.

I hope I will soon be able to read your second part. At this point also I would be interested in the overall chapter structure, just as headings, table of content? have you posted that already or have I missed that? I wonder if you have a chapter where you explain the framework for all the three case studies? Eventually at some point in the future, the thesis or chapters of it should be published in the open tnl, as you did work that others will benefit from. It also ties in with some areas of my thesis and if you finish earlier, which I hope will be the case, I can quote you;-)