Train travel between warsaw and bern?

We would like to travel by train between these cities:
Warsaw to Prerov, CZ (3 days in prerov)
Prerov, CZ to Bern, Switz

It would be great to have a two day layover somewhere in Germany between Prerov and Bern.

Any suggestions? This is one way travel. We don't know which city in Germany would be the best for us for sightseeing and the best for travel onto Bern, never been to germany before.

We couldn't find any packages via eurorail or any other passes.

Any suggestions

Thank you - we would appreciate any assistance..