Could you use the framework that's there and have each popup layer contain an iframe to the content that is supposed to go in it and then within the design of the iframe'd content, have that have the additional page title and all that? I know iframe's are a little wierd regarding the way SEO applies, but as I understand, as long as the content that is being included in the iframe has links back into the main part of the site and they are located in the same site (not google or some forum or whatever), then they can be indexed.

Would this make them extra pages but still make the design work the way it is?

Sledger (I think) posted an example of something like this in his Star Trek looking example a little while back.