"I would imagine a train ride would be quite long whereas a flight would be fairly quick. "
Such a common misconception. They rarely build airports in downtown areas. Usually you've got travel from downtown to the airport, then from the next airport to downtown. Then you have time waiting in line to check in, going through security, getting to the gate, waiting to board, boarding time, flight time, deplaning, waiting for luggage at the carousel, finding ground transportation. Actual flight time is a small portion of the total trip time. In the case of Paris to Munich, you can count on about 45 min from downtown Paris to your terminal at CDG, just to start waiting in lines. In Munich, even without checked baggage, I can't see getting to the S-Bahn station in less than 20 minutes and from there it's 40 minutes into downtown. If you fly, the time you spend on commuter trains will be about 20% of the time it would have taken by train all the way. You'll still probably spend more time on trains then you will in the air.
BTW, the train that goes from Strasbourg to Stuttgart skirts the northern Black Forest. If you don't care about getting the lowest fares, you could go through the Black Forest from Strasbourg to Stuttgart and spend the night in Baden-Baden or Freudenstadt.