Not too sure on terminology, but just to clarify when I say main forum index (or something along those lines), I mean this
http://www.atarnotes.com/forum/index.php and when I say board index, I mean
AnnouncementsI reckon ditch the regular web forum design for the main forum index page altogether and have something more consistent with the site design for these parts of the site
http://www.atarnotes.com/?p=books http://www.atarnotes.com/I think the main thing that makes the main index confusing for some people is that you have to scroll, and scroll until you get to say the VCE subject boards, which might end up being pretty easy to miss. So I think simplifying the design of the main index page is what should be done.
Instead of having rows and rows of boards listed in traditional web forum style, I think something minimal would suffice e.g. perhaps just boxes labelled with the name of the board, which then link to the regular board index pages.
ATAR Notes Publications
Administration
National Education
VCE State Forum
which then expand out to have more boxes that link to the subboards. Those could be organised so that one group of boards (e.g. National Education and General Discussion) are located next to each other. Here's a rubbish MS Paint picture to try and show what I'm getting at, well the gist of it anyway.

The actual grouping of the boards wouldn't need to be so strict, you could have all the ATARNotes books and admin boards by themselves at the top, and then go into the grouped collection of labels when it gets to the VCE, HSC etc. boards.
Maybe not something that expands out or is overly flashy, but just something that compresses the main index page to be easier to navigate without being a cluttered mess, and something that makes it obvious where the VCE subject boards are, and where the buying and selling boards are etc.
We don't really need the "last post" since that's kinda broken on the main page anyway e.g. the thread listed here isn't the latest post
http://www.atarnotes.com/forum/index.php?action=collapse;c=21;sa=expand;af732870e016=e18fc5c05cf96ab83062250621581d5c#c21)/. Nor do we need the numbers saying "12893128" posts in this board, we can do without that knowledge on the main page.
Most of the browsing would be done through the recent posts at the bottom (that could be placed somewhere else?), using either the unread replies/posts or actually clicking on the board and browsing that way. Having the search function more prominent would also be nice.
I think the structure of indexes (indices?) for each specific board is probably fine. That probably doesn't need to change. But I'd imagine if other pages on the site are changing, then those pages too would have small alterations made to keep it consistent with the design used for the rest of the site. I think doing that would fix some of the problems people were having with those pages, e.g. changing the "new topic" button and hence making it even more obvious that it's there. The "last post" etc. stuff is more useful on boards like that
Mathematics/Science/Technology so I don't think we need to get rid of that like I suggested for the main index page.
What about a mini-tutorial that happens after sign-up and can be accessed again in the future?
Just generally like, showing pages with red circles around, say, the English board, with text saying "This is the English board. English goes here", then they click "next"... "This is the chat button. Click here for sex chat"
Of course, it would be more helpful than my example, and perhaps there could be a "learn more" button that took you to an entry about that forum or button or whatever else that explained it in depth for the extra-confused (would be a bit of work for the Mod team/writers and David I suppose).
Yeah I really like the idea of a guide, you could explain LaTeX etc. there too.