My family is planning a very similar trip for summer 2020. My husband and I are traveling with our 17 year old daughter and our 14 year old son. We also found an extremely good deal on round trip tickets to and from Paris for 24 days total in June.
We plan to start in Paris and make a bit of a loop starting the Alsace region, travel through southern Germany and Austria, and then go back into Germany making our way back to Paris. We are not planning to visit Switzerland, because I hear Switzerland is expensive and we plan to see the Alps in Germany and Austria. I am still working on our itinerary, but do have a first draft that I would be happy to share. It sounds like your trip is a little shorter than ours, but I thought that you might be interested in seeing our itinerary, and you can adjust to fit your timetable.
I also have the goal of keeping travel days to around 4 hours a trip, and we also are hoping to travel mostly by train. But our current itinerary does have some legs that are significantly longer than 4 hours by train, and the train routes between a few cities are not ideal. We are considering renting a car for at least part of the trip, and that would get certain sections of the trip to a more reasonable travel time. Again, my itinerary is a work in process and is truly a first draft. I am sure it will be changed several times before we finalize it!
Day 1: Flight to Paris, overnight flight
Day 2- 5: 3 nights in Paris
Day 5 - 8: Travel to Colmar, France, 3 nights
Day 8 - 10: Travel to Freidburg im Breisgau, Germany, 2 nights
Day 10- 13: Travel to Fussen, Germany, 3 nights
Day 13 - 16: Travel to Innsbruck, Austria, 3 nights ( I believe there is an alpine slide in Innsbruck)
Day 16 - 19: Hallstatt, Austria, 3 nights
Day 19 - 21: Rothenburg od Tauber, Germany, 2 nights
Day 21 - 23: Baden Baden, Germany, 2 nights
Day 23 - 24: Stay in or near Paris, Fly home
I know you mentioned you would like to stay in Munich, so you could easily skip Hallstatt and replace it with Munich. That would make the travel time more manageable as well. We are considering either daytripping into Munich or adjusting the itinerary a little to allow a couple nights in Munich.
Good luck with your planning, I am sure your family will have a great trip!