The website for the City of Minneapolis contains some very interesting Information Architecture decisions. The generally repetitive and scattered nature of the site can only leave one to imagine what the wireframe of that site looks like.
Organization could be improved in many ways. I would first change it to a two column to reduce clutter and eliminate the style of the current news feed. I would also eliminate the repeating tool bars. They contain identical information and are just redundant and confusing. I would like to model my organization after the City of Chicago's site. I feel it is much more usable and effective.
The layer is also intersting. Some of the links take you to completely different sites unrelated to the actual City of Minneapolis site. This makes it much more confusing because your toolbar changes and is different for each site and you cannot always access the information you want to.
I like your idea to reduce the redundancy of links by having one central nav bar rather than two. Do you think you will use the top nav bar or left nav bar? I agree too that the inner pages have their own nav bar which makes things very confusing. Perhaps you could focus on one of those inner pages as your second page for the class project, and demonstrate how you might clean up the navigation confusion?
One other idea: I agree with you that the site map of this web site is all over the place--kind of like the "web" model of a site map. Might you try to aim for a more "hierarchical" site map model? I look forward to seeing your revision.