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Two Week Holiday - Germany, Switzerland & Austria - Confused where to start

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We are planning on a two half week vacation flying from Ontario. I am not sure logistically would be the best way of doing the itinerary we have in mind and would love any information or guidance. Just in the first stages of the fun - Our wish list is the following:
Munich - doing day trips - Dachau, King Ludwig's Castles; Nuremburg; Rothenburg.

Austria - Salzburg, Vienna and Halstatt.
Switzerland - Staying in Interlaken, going up Schiltorn ; perhaps see Lucerne. We are not counting the days we fly in or out of Europe as our actual stay in Europe.

Now my problem is where to fly into and out of for trip in and out of Europe and which order logistically speaking would be best in saving time . Using trains our whole stay and planning on getting the Swiss and German passes.

Big question is do we start in Germany from Canada - then Austria doing Salzburg, Vienna and then Halstatt and then Switzerland? Would you travel to Switzerland from Halstatt or Vienna? Or would we do fly into Vienna and then do Germany and then Switzerland and fly home from Zurich?

I am a bit confused and would love the experts to chime in - thanks so much.

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My family and my sister's family did almost this exact trip several years ago.
We flew into Stuttgart because there were bargain fares there at the time, but Munich is fine too. You can compare fares by looking at the map at google.com/flights

The most logical would be to fly into Munich and out of Zurich (or Geneva) and conduct your trip from Munich to Salzburg to the Swiss alps. You can compare the cost of this "open jaw" flight to in and out of Munich, for example. Open jaw costs more in general, so you'll have to decide what using an extra day just getting back to Munich is worth to you (time, energy, train costs).

In any case, you may want to consider cutting down the number of places you want to go, especially if they are some distance away. Each time you do that you increase your stress and increase your time sitting on a train. If you read a lot of the advice on here, it is to not try to fit too many places into your trip. As Rick say, "assume you will return". So personally I'd skipping some or all of Rothenburg, Nuremburg, and Vienna. There's a lot to do in and around Munich, in and around Salzburg (Google "Eisriesenwelt" and "Eagle's Nest" and "Konigsee" and "Sound of Music tour")
You can do Halstatt in one day using the train from Salzburg, but it will be a full day.

The longest train ride in your trip will be from Salzburg to Zurich, about 6 hours.

When we went we spent a WEEK in the Swiss Alps, and there's easily enough to do for 2 weeks. Do NOT stay in Interlaken--it is nothing compared to Lauterbrunnen, Murren, Wengen, or Grindelwald. Google image all those to see why. I'll send you our dozen favorite walks in the region so you can see why one can easily spend 2 weeks there. Click on your name in the upper right to view your mail here.
Whatever you decide, you'll want to nail down your accommodations ASAP.

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