Is your hosting really in Houston? If so, that’s probably why your SSL times are so long. SSL takes 2 or 3 round trips for the negotiation (can’t remember off the top of my head) so the latency really hurts.
On the caching, there are probably 2 main differences. The first (and main one) is that you need “cache-control: public” headers on the responses, otherwise IE won’t cache them when it’s over SSL. The other is that WebPagetest closes the browser between first view and repeat view so it’s more like someone coming back later in a different browser session than someone bouncing around the site.
On the recommendations front:
Finally, it looks like you have a sprite for the panes but there are a bunch of icons and graphical elements that could benefit from being sprited together: http://www.webpagetest.org/pageimages.php?test=100514_N7Q&run=1&cached=