Hi Marta,
for 5 days you plan quite a big program 😅
if you tell more about your interests (museum, hiking, ..), will be easier to give an advice.
in general some interesting places: Bornholm (ferry from Ystad, where you should be also able to catch one to Poland), Gdańsk, Hel in Poland.
Copenhagen is also always worth a stopover but it is an expensive place.
If you want to spend more times in cities than on trains and ferries I would recommend you to go from Germany direct to Poland and then spend some time there (Szcecin, Swinjouscie, Gdańsk, Toruń, Wroclaw) and go from there to Czech Republic.
