I started to set up my portfolio site over winter break, basically by picking a theme and populating it with content. You can find what I have done so far at http://jonathanvit.journalism.cuny.edu/.
Going forward, I plan to reorganize my clips, choosing eight to ten examples of my best written work in both print and online and making that my main portfolio. I feel like there are currently too many articles, many of them examples of recent, but not particularly exceptional work. I did this to show that I was working while in grad. school, but I like the idea of running a blog on the site better.
Also on the schedule: Customizing CSS to remove the wood grain background on some pages, changing the color scheme, writing my resume in wordpress instead of linking to Linked In and shooting some more multimedia work.
It’s an impressive theme for strong visual material, something you might want to consider reinforcing in your menu/nav. If you feel there’s too much material of quality that’s secondary, try using a visual hierarchy in your archive pages to distinguish your best work (i.e. top work gets a thumbnail image, secondary work just a link). I like the tweaks you suggest. I’d also explore whether the theme allows better use of the right sidebar for things like tag clouds; it may clutter the look, but may also make access points for content easier. Nice!