It should be noted that the Bayern-Böhmen-Ticket, like the Bayern-Ticket, is an all day pass for regional trains, which do not have seat reservations, so advance purchase is not necessary. The price for two travelers is 30,50€. The Bayern-Böhmen-Ticket will take you as far as Pilsen; use Czech Rail tickets for Pilsen to Prague.
There are four direct trains from Munich to Prague per day leaving Munich Hbf at 4:55, 9:01, 12:44, and 17:02. They take 5¾ to 6 hours. I've been told, but cannot confirm, that you can purchase the Pilsen to Prague ticket on the train from the conductor in the Czech Republic for about 100 Kc (less then 4€/person). I'm not sure if the conductor takes euro.
Advance purchase tickets, which start at 29€/person for the bus from Munich and go up as the lower priced tickets sell out, can be either a Bahn Intercity bus from the Hackerbrücke ZOB or an ICE to Nürnberg and IC bus from there.
As for Prague to Berlin, you can make a stopover in Dresden, but it has to be for a specific duration (in two hours increments) in Dresden. The Eurocity train runs every 2 hours from 6:29 leaving Prague. The 18:29 connection is an IC to Berlin-Lichtenberg station and an S-Bahn from there.
