Here's my 2 cents. When I say Section I'm referring to the grey collapsible space in which sets of Orange links (Categories) appear. General train of thought is getting things organised to roughly how other forums tend to lay things out and getting certain categories into the right visibility (as in, when you click into the page the stuff the user should see first).
***
'Read this first!' Section: Should probably have a different name. Main, maybe.
Announcements should be at top; that's fine. '& Site Development' instead of 'and site development'. Announcements & News can also work as a name. This category should always be at the very top.
FAQs & Tutorials category should be removed from here and split into game-specific FAQ/Tutorial categories under the FF7, FF8, FF9 sections to keep things organised by game.
Archive should be right at the bottom of the home page; only long-time users or people rooting around looking for old ASM posts are going to be interested in this category. Could go in its own section, so long as it's right at the bottom and not taking visibility priority over anything else. Should not be in the top section.
Qhimm Wiki: This is probably fine in the top section, though it'll only be of real interest to assembly enthusiasts/modders rather than regular users. As it's a redirect, should appear below the other categories that lead into child boards so it's fine where it is.
Discord: Ditto, should always be in this top section as you will want new visitors to also use the Discord channel.
FF7,8,9 Section
I saw it mentioned that this is still WIP, but I'd suggest moving Other Mods below Gameplay as it's strange to have a Misc section appear above a specifically-titled category; Other Mods is a catch-all for ones that don't cleanly fit into the others. Audio > Graphics > Gameplay > Other > Tools (or Tools at the top as it is now) feels like a good order, as Tools is a different kettle of fish with a different user-base.
Troubleshooting and Scripting/Reverse Engineering categories should be added for each separate game with some of the more recent threads sorted in. But there are a lot of threads to sift through so it would be practical to stagger out a move (if one is made) over a longer course of time. But ideally these should be organised by game rather than as a mass away from their respective FF sections.
A section for Misc games might be prudent as we get posts about non-FF games occasionally but probably not with all the categories that the three FF game sections have.
Final Fantasy Forums Section
The four sections of mod types will need to be removed from here as duplicate sections will result in threads being posted in two different places.
General Discussion should move to the top section.
FF7NX/FF8NX Driver; this should be under Project Forums section as it doesn't cleanly fit in either FF7 or FF8. With this and the others moved, the FF Forums Section can be retired.
Off-Topic Forums
Only has Completely Unrelated, which should move up to top with General Discussion and appear above or below it (so long as they're together); this empty section should then be retired. It feels like Completely Unrelated should have been called General Discussion, while the old General Discussion should have had a name like FF-Discussion or something. A compromise might be to rename General Discussion to FF-Discussion and keep Completely Unrelated's name; that way new users don't get confused as General Discussion implies 'discussion about general topics' (which is what Completely Unrelated is currently for) rather than specifically FF-topics.
Project Forums
This will be tricky to place. It should either go above or below the FF sections. An alternative is to make this section into a Category that appears in the top section, with each Project appearing listed inside it as a child-board (with the exception of 7th Heaven, more on that at bottom).
Another possibility is trying to place them within their respective FF Section categories as child-boards (Team Avalanche to a child-board of the FF7 Section's Graphics category for instance) though it'll be tricky to place projects that cover multiple games like the graphics drivers this way.
Whatever sorting is used, 7th Heaven should go to the top section as a category visible from the get-go because it's a fair bet that new users turning up to Qhimm are aware of 7th Heaven and/or intend to use it so having immediate visibility of it will be beneficial. It's also a huge sub-board and has a lot of activity. Not sure where it'd be placed; either above or below the two Discussion channels.