Hi Naryet,
My wife, adult daughter and I did a similarly themed trip this past December, from 12/9 to 12/30. Our route was Bruges-Strasbourg-Munich-Salzburg-Budapest-Vienna-Cesky Krumlov-Prague, so much of of your trip in reverse. We also daytripped to Nuremberg from Munich. We spent Christmas Day in Vienna, so the last two stops (in Czech) were post Christmas. All of our travel was by train except for the link from Vienna to Cesky, for which we used the minivan service of CKShuttle (because it was Dec 26 and regular train service was altered). I like that you you have relatively long stays in all places. That was my plan originally, but when we thought about doing a day trip from Munich to Salzburg, and another from Prague to Cesky, I came to the conclusion that it would be better to do one night stops in those two places than to visit them for the day and then a day or two later pass right through them on the way to our next destination. I’m glad we made that compromise. Salzburg turned out to be our favourite Christmas market town and it was nice to be there for the evening without having to catch a train back to Munich. In fact, we would have loved to have two nights there, but we made excellent use of our 24 hours. One night was enough in Cesky (the market was still going on the 27th), and we caught an early afternoon train directly to Prague, so we essentially had two half days there too. I guess my point is that you should seriously weigh the pros and cons of daytripping to a place which is on your route versus doing a one night stand at that place. (I should add that we are all light, efficient travellers who don’t subscribe to the belief that it takes a half day to check out of one place, and another half day to check into the next.) The other point I would make is to include Salzburg, either as a stop or a day trip, if it is not already in your plans. Whether it’s good or not, that’s my advice.