I decided even to dispatch with the header bar, putting navigation at the bottom of the main page; presumably, people will only care to see more of my writing if they've read the article. Not as good for people revisiting the page, but they can likely remember http://jmoiron.net/blog or bookmark it in order to get to the search.
My fonts are slightly smaller and slightly less contrast, and after looking at Gemmell's blog I wonder if I should change that decision. I wanted to have emphasized elements of the text easily distinguishable from the body while not distracting.
Also, I agree with Gemmell's "The basic tenets of hypertext should be left alone". One of these basic tenets, to me, are the semantic meanings of Blue, Purple, and Red text for normal, :visited, and :active hyperlinks. If you want to chose a link color, do not invert or violate these classical meanings.