It sounds to me like a trip of a life time. However if it were me with small kids I would possible skip some of that stuff, They are simply too young to understand a lot of the history. Instead maybe plan for the black forest region. Lots of interesting places to see and things to do. Also plan a couple days on the Bodesee where there is a museum in the air ship museum and Manau Island.
Also, remember if you think one day to drive, plan on two. Travel in Europe is nothing like here. Although there are freeways, they are simply not as interesting as the back roads. Stop often to explore the fantastic foods and history of the country.