Any ideas on the best way to travel between Murren Switzerland and Cesky Krumlov this coming Sept?
The Swiss will route you to Bern/Zurich HB/Ceske Budejovice/Cresky Krumlov. On one run, the train from Zurich HB to Ceske Budejovice is a sleeper. It's a 14.0 train ride. There is also a day train that departs Interlaken Ost at 8:01. This journey requires 4 train changes and will take 15.5hrs.
You can see these trains on www.bahn.de. Put in Interlaken Ost as your departing location as the system will not see Murren.