Originally Posted by
You want to go where?
otherwise known as Bankfurt is not worth stopping in, so your idea of either using it as a transfer point to go to Heidelberg or using the airport to rent a car to go to Alsace is a good one. That said, Alsace is worth a week on its own!
Alsace is actually quite a detour from Frankfurt and if the OP wants to see Amsterdam, Munich and Prague not worth the hassle IMHO. Cologne is a very good suggestion as it is directly on the way from Amsterdam to Frankfurt and on to Munich and worth a stop. You will be right in the middle of the town as mentioned before and can easily explore the city and see the cathedral. Cologne - Frankfurt is just a bit more than an hour and you can then catch a train to Heidelberg which takes you another 50 minutes. From Heidelberg to Munich it is another ~3 hours and you have to connect in Stuttgart which is quite a pain these days as there is construction work going on there.