I would start out with 2 nights in Ruedesheim (Rhine Valley), where one can take a gondola over the vineyards, and take a Rhine cruise perhaps as far as Koblenz, and perhaps visit the Cologne Cathedral as well as part of that day trip (boat and train combo concept works well). Then I would proceed to Berlin for about 3 nights to experience the vibrant capital, and start by using bus routes 100 or 200 to get acquainted with major sights. Finally I would spend 3 nights or so in Munich, with, among other things, an opportunity to visit the Neuschwanstein Castle near Fuessen and the Hofbrauhaus.