1) Yeah I was suspicious about suggesting that you remove the border because I've had that experience many times when I think that something would look better if I changed it, do so, and then gasp in horror. I was thinking about the empty space so I'm not surprised you said that.
One solution, that I don't know if you've already thought of, would be to change your css so that the site takes up a relative percentage of the screen instead of a fixed amount. You only have two columns so it shouldn't be too hard to do. You have a header, a body, and a footer. You could let these things take up about eighty percent of the screen maybe, or more or less - whatever. Then, within your body you can make the the sidebar a fixed width, and the content fluid. That way you don't mess up your navigation and the content's width will expand or shrink to fit the leftover room. You can also set a minimum width beyond which the content will not shrink, if you're so inclined.
That way your site will look good on any size computer screen and you don't have to worry about the negative space. Maybe you already thought of that and rejected it for some reason, but if you just don't know how then I can try to help you.
2) Speaking of font, I don't know if you've seen my site when I kept asking people for help but if you look in the comments section under the post "This site is under construction" there is a little debate about font between me and someone from here who went to take a look. Basically we were talking about the difference between a site that looks professional and a site that looks personal and I was going for personal.
You can read the long boring explanations about reader studies and personal preferences there but the gist of the conclusion we reached is that Verdana is consistently ranked as easier to read by viewers and is widely available on most computers. Since you're having problems with the white (gray) on black background you might want to stick to an easy to read font like Verdana. Definetely sans-serif, though whatever you decide. Serif fonts are not recommended for the web because they are harder to read on screen (easier in print).
For my own site I chose Trebuchet MS and Comic Sans Ms. Trebuchet Ms is similar to the popular Arial, but said to convey more personality by those who purport to know these things. It's a bit sassy. Comic Sans Ms is another font with loads of personality and is a real attention getter that was developed to be used for comics and I think it conveys a humorous tone very well. I did think it added more visual appeal and created a more friendly tone to my site after changing the font. But I had to increase the size slightly to compensate for not having chosen a very neutral font.
So basically I'd think about what you can do with Verdana, Comic Sans MS, or Trebuchet MS. If you don't like any of those, the long discussion about various fonts and their merits or demerits can be found in those comments on my website.