In order to see exactly how far I could go with themes, I replaced the screen.css with my own, and prefaced it with a css file that pretty much wiped everything. And yet. I still had some of my a hrefs in light blue for my header, which I didn't want.
So in looking into it, it's the superfish.css file that's STILL overriding my css. I'm not sure if I have a suggestion to anything, though, since I'm assuming the superfish css is needed, but it's mucking with layout in a way that makes it really hard to make a 'blank' theme to start hacking around in.
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One alternative is to get rid of superfish and use a different method for theming the menus. They're basically unordered list elements so there are probably plenty of menuing solutions you can use.
We will eventually put out a stone simple theme that you can use to build up from, instead of having to tear stuff out of what we have now.