> Third, you need to constrain text width. It's a lot of work to scan 1000 pixels for each line.

It's funny you criticize that, because it's one of the only parts of my site design that I actually have A/B tested: http://www.gwern.net/a-b-testing#max-width The smaller widths did not do well.

> Books are also not backlit. If you want to recreate the experience of reading a book, use a slightly off-white color and a dark colored ink (for example, a very dark blue or brown).

Hm, this sounds plausible.

    html {
      background-color: #FCFCFC;
    }
    
    html, a {
      color: #303C3C;
    }

Done.

    blockquote {
      font-style: italic;
    }

No; I use blockquotes too much and they're too long to make them italics. The background shading seems like enough for now.

    #header {
      margin-top: 50px;
      margin-bottom: 30px;
    }

I'll try it.

    #content {
      width: 550px;
      margin-left: 200px;
      padding-left: 0;
      line-height: 150%;
    }

Duly stolen. And the TOC changes look like an improvement too.