Everything works okay now: primary and secondary canvas update, changing zoom works for both, drawing on colordex updates correctly..
Hell, since you said everything, I'll try some other stuff:
* All items in select menu appear to work, when I manage to actually 'click' them instead of dragging the window around
* Actually, that's a general issue with using the menus, they detect drags rather eagerly, though I don't know if anything can be done about this on the Javascript end.
* Copy and paste work as expected, as does Insert clipart (well, I wasn't sure what to expect with Insert Clipart, but the way it works makes reasonable sense)
* I'm not sure I understand playback correctly .. I expected this to play my 2-frame animation, but it prompted me for a file.
* Actually, I see now that animation playback is controlled by a button on the Frames window, which appears to work fine.
* frame 'links' appear to work as intended, affecting the display if it is set to linked
* I found the frame/layer opacity control but I couldn't find a way to reorder frames, I guess this is either disabled or not implemented yet.
* Undo navigation works okay but occasionally causes the update of the primary viewport to be disabled (I THINK. If this is not the cause on its own, it may involve manipulating undo history and then changing primary viewport display mode to Frame). It can be reenabled by resizing the primary viewport.
* Magic wand -- allows me to freely drag around the selection. This is a GREAT tool, but not at all what I was expecting from the name or icon.
* Lasso works fine. I'd just like to suggest the option of using
Winding aka Nonzero fill rule instead of even-odd (the result of this is that no selection ever has a hole in it.). This is natively supported by most polygon rasterizers I know of.
* The Tile, Remove Tile, and Collision tools don't function usefully. I guess I have to setup tiles first

* Zoom tool works okay; I'm not sure precisely what hand is supposed to do -- Just control where the canvas is shown? If that's it, it's working fine.
* Clicking on the canvas to draw during animation is equivalent to using Hand tool. This is understandable, but nonetheless, kind of surprising and hilarious.
* Eraser and colorpicker work
* Magic eraser and brush work, I guess? Maybe I don't understand the colordex well enough yet, I get a sort of colordexy output but I don't seem to reliably be able to move towards one color or the other. I consider this PEBCAK.
* Palette scan works, in either mode
* Export seems to work okay, both PNG and GIF, as do Open and Save.
* Grid appears to work (it's just an overlay, right, it has no active function like snapping?)
* soo. I think that leaves Playback, and New from Playback, which I basically just don't understand so I can't meaningfully test.
* EDIT: Oh, and I saw that middle-click-to-pan was added a few weeks ago (looking at the PJ thread), so I tested that.. It doesn't work for me
Re: wacom plugin:
The unofficial plugin is designed to have the same api as the official, so hopefully there shouldn't be much work involved in supporting it fully. Installing it is already enough to get rid of the warning message.
EDIT: I see that, from your posts on PJ, colordex actually constructs an ordered adjacency graph of the colors. Dunno if that's good for anyone else, but that is the most straightforward explanation of actual colordex function from my POV.