1) Is is possible to incorporate a custom mood theme into the s2 code? I suspect the answer is no because LJ needs to handle it directly so that it can be accessed on the posting page (like userpics and tags), but I figured asking would be the best thing to do.
2) I can't find code for the links list in the sidebar. I'm pretty certain that can be incorporated into the s2 code, since header links can be changed that way, but I can't find the code for it, nor can I figure out where in my custom layer I should put it. (This one I feel rather silly asking about.)
I'm currently not using the custom layer/style, so, thankfully, these issues aren't making my journal wonky. In case it's useful, the layer I'm working on is here. It's based on this, which is code provided by grrliz for using Mixit/Expresseive layouts on Dreamwidth. With my personalizations (which aren't yet finished), the code probably looks a bit like Frankenstein's monster, but so far it seems to work fine on LJ.
3) Lastly, while I'm here, I was wondering if you knew of any resources that would be useful as a kind of s2 dictionary so that reading the code would be easier. Something similar to what you did for CSS, maybe, but with just the descriptions, no pictures?