From Munich a trip to Salzburg appears to be a "must" for most Americans (can be done by train). A trip into a Alps to Garmisch and Neuschwanstein (should be done by coach) could be an idea, too. Beside that Munich will offer more than enough for your days. For Berlin a day trip to Dresden (by train) is a really nice to have and a day in Potsdam (20 minutes by train) is mandatory. Regarding Frankfurt: Heidelberg appears to be another "must" for Americans I never understood why). From the three cities you mentioned, my first choice (with wearing my American pair of glasses) would be Rothenburg, Würzburg and Heidelberg as a runner up. If you need detailed help, PM me.

Thomas