Germany, Austria and Switzerland Ideas for sites, travel schedule and transportation

I would keep it simple ...
Munich (4) > Salzburg (2) > Hallstat (2) > Lauterbrunnen (4) > Luzern (2) > Zurich to fly out

The Glacier Express would add a lot to your logistics ...
Munich (4) > Salzburg (2) > Hallstat (2) > St Moritz (1) > Glacier Express > Zermatt (2) > Lauterbrunnen (2) > Luzern (1) > Zurich to fly out

Your wish list for Munich ...
(Neuschwanstein Castle train and bike trip, Dachau tour, authentic German tours (brewery/food) through town)
... requires at least 3 full days, which means a stay of 4 nights.

Why Lauterbrunnen for 4 days? What do you suggest to do there?

In Lauterbrunnen you are deep up a valley with mountain railways and lifts on either side (Murren, Grindelwald, Wemgen) for summer alpine walks. You also have the Jungfrau Mountain Railway. Most people schedule a few days as an insurance in case whether is unfavourable.

My personal preference is to travel by car, but I believe that the places that you have listed can also be done by train. In fact some of the towns in the Lauterbrunnen area can only be reached by train. The reason I prefer to travel by car is that I can leave when I want, take the route that I prefer, stop whenever I see the makings of a beautiful photo, eat wherever and whenever I want and, in short, ignore schedules set by others.

If you decide to rent a car in Munich, Neuschwanstein, Salzburg and Halstatt are all easy drives. I would recommend NOT taking the autobahn to these three towns as the back roads, especially the Alpenstrasse (Fussen to Berchtesgaden) are particularly beautiful - many pretty little towns, beautiful lakes and, of course, views of the Alps.

I would recommend spending three, maybe even four nights in Salzburg. Spend one day in Salzburg walking around the town, visiting the Hof, doing the Sound of Music tour, one day in Halstatt and the extra day going up to the Eagle's Nest and visiting the Documentation Center in Berchtesgaden.

Vienna is a beautiful city with lots to see. I would say you would need at least four nights and three days to enjoy it.

If you do go to Alsace you should find Riquewihr and Colmar particularly beautiful. If you are car nuts you might want to add Mulhouse's Cité de l'Automobile to your list. It has an extensive car museum and a particularly good collection of Bugattis. The town itself is said to be worth a visit though I have only seen the car museum.

Lauterbrunnen Valley is beautiful. One trip we stayed in Murren and hiked the Children's Adventure Trail and along the valley floor in Lauterbrunnen. The next trip a year later, we stayed in Wengen on the opposite side of the valley. We hiked the Northface Trail above Murren and the Mannlich to Kleinne Scheidegg trail and took the train back down to Wengen. The views from the our apartment in Wengen was amazing. We would watch the sun come up and go set on the far side of the valley Murren every day. The scenery was amazing. The hiking was easy enough for a 7 year old.

If you're going to the Berner Oberland, I would definitely recommend 4 nights in the area. There's lots of options for hikes, walks, and lifts, on the valley floor and up each side. In addition, the weather there is both unpredictable and changeable, as it always is in the mountains. So, you want a hedge against rain or clouds. I stayed in Mürren and was very happy with my choice, but others prefer Lauterbrunnen (in the valley), Gimmelwald (on the same side as Lauterbrunnen, but smaller and lower down), or Wengen (largest of the four, up the other side).

As for what I did, on my first (half) day I went up the Allmendhubel. The second day, I went up the Schilthorn and walked around Gimmelwald. The third day, I went up the Jungfraujoch, and went for the afternoon to Interlaken and saw the Museum of Tourism and the many large tour groups. All of these days had basically good weather. The fourth day it was cloudy with occasional light rain, so I walked the valley floor and saw the Trümmelbach Falls. There's plenty more to see and do there - these are just the obvious and easy highlights. I loved every minute of it, and would go back in a heartbeat. Just bring lots of money, or plan to get all your food from the Coop grocery stores in Mürren, Wengen, and Lauterbrunnen (Interlaken has several large grocery stores, at various price ranges).

Salzburg is easy from Munich by train. Adding Hallstadt, Neuschwanstein and Berchtesgaden would be a good reason to rent a car. I'd probably schedule your itinerary so you can include only a few days with a car and return it in the country where you picked it up.

Remember you only have two weeks, which disappear quickly when you are on the road. Don't think about how much you can add to your trip. Think first about what you hope to see in each place and make sure you give yourself time for that, then prioritize based on where you would like to visit most.

If you are up for driving then I agree a car would be best for about 6 nights from Munich.
First to Salzburg, then Halstatt, Berchtesgaden, and Neuschwanstein, before returning the car in Fussen and heading on to Switzerland.