Berlin is kind of a hike to get to both from Prague and from Amsterdam. I would focus on adding a third city that's closer to one of those two, maybe Paris or Bruges? Munich might work. I combined that with a trip to Prague many years ago (15+), but I can't remember if I took the train directly from Prague or what the distance is.
I have some Merrell boots from a few years ago that I wore to death through two rainy Parisian winters.