You're 99% correct... the content pulled into the panes via JS won't really accessible to the SERPs, but the index page will be optimized (though it's not done yet).
In any event, I'm not really worried about SEO for this site. While I know that's like heresy in website development, I'm not planning on targeting organic search as a means of building business. In my experience, 'freelance web development' and similar terms related to my site are next-to impossible to rank well for, and so I'm going to focus on finding clients by other means (namely personal contacts).
Thus, the purpose of the site isn't to tout my website development skills -- it's to demonstrate a custom web application which I could build for anyone. I know someone will disagree, but those are two completely different customer segments.