Your itinerary is very hectic and while you’ve picked a reasonable circle route for a longer trip, the cities you’ve picked are pretty far apart.. Travel time is really going to cut into this. Berlin to Prague is nearly 5 hours on the train and most of your trips are in the 7 hour range by train. Any flight (when you add in getting to and from the airports, check-in time and security time) takes a minimum of 4 1/2 to 5 hours and a flight in the middle of the day cuts out the entire day for sightseeing. I would cut one city in an attempt to make this more doable.

I’m not sure what to recommend for transportation. Train is usually my preference but you may want to fly from Berlin to Prague and take an overnight train from Prague to Munich (or vice versa). One overnight train and one in-Europe flight is about the maximum for a 14 day trip. A 5 day select pass for Benelux, Germany, Switzerland and France and point to point tickets (or a cheap flight) to and from Prague may be your best bet financially for this trip.

BTW, there’s a train station (and numerous hotels) at the Amsterdam airport, so you don’t have to go into ADam at all on one end of your trip.