So, let’s play:
Day 1 you arrive about 2pm jet lagged. Night
Day 2 you see Munich
Day 3 you take a train 10am to 4pm by the time you get to the hotel and check in, lets call it 4pm
Day 4 see Prague
Day 5 Train to Vienna 10am to 3pm so you will be checked in by 4pm.
Day 6 See Vienna
Day 7 Train to Budapest 10am to 1pm
Day 8 See Budapest
Day 9 Train to Krakow 10am to 7pm check-in eat and go to bed. You can fly and that will save maybe 3 hours if there is a flight with a good schedule. on your travel day.
Day 10 See Krakow
Day 11 Tain to Warsaw 10am to 1pm.
Day 12 See Warsaw
Day 12 Depart.
By my travel logic, using the final weekend, 2 weeks is 16 days so you have 4 days to play with. Its personal taste but I would put them in Prague, Vienna, Budapest and Krakow. Of course, again personal taste, I would drop Munich and Warsaw and add those nights to the the other cities and then I think it would be a trip that I would do. As it is, too much too fast and too much time in transit vs seeing things.