It's not often that I do a full tech post, mostly because I find that philosophy and human behaviour tend to have a larger target audience. Having said this I've been hacking this thing for the last 8 hours, and I've finally got it right. So I'm publishing so that others can avoid my problems.

It turns out the latest version of the MacTeX LaTeX package comes without a critical set of files. You can however install the tex4ht source files here.

You also need to install your font files in the following directories:

/usr/share/texmf/fonts/
/usr/share/texmf/tex4ht/ht-fonts/

Run a updmap-sys and then run a texhash so as to update your ls-R files.

I'm finished, I've been staring at this problem all day, and feel like I've wasted a day doing so. I realise that I can now get to what I needed to do tomorrow (or the day after, depending on what the day brings).