This is quite unreadable with the low contrast colors and the columns are much too small. If you pick a random paper on the arxiv[1] and imagine how much vertical space it will take to just to show the text you'll see the problem.
I think you're right re: contrast, but I'm still conflicted about column size. On the one hand, a wider column gives better justified results, but on the other hand, it makes the sliding figure column more difficult on 13 in. Screens. Which did you find more beneficial, wider columns, or sliding figures?
Contrast[1] is too low for me as well, and text should not be justified[2] IMO.
I too appreciate your effort, but keep in mind the differences between print- and web- layout design. Most scientific papers are published in PDF, using Latex. These two work great for the print. Correct hyphenation, good justified text, etc. Browsers are not that far yet, unfortunately.
[1] http://arxiv.org/list/hep-ex/new