I am having difficulty finding a Eurorail pass that covers travel in all of these countries. Does anyone know of a train pass that covers all three countries
There is a New German-Czech Pass, but condering the rail fare is very inexpensive in the CR, personally I would not buy it.
Study Rick's pages on Rail Passes.
I am traveling to Germany, Czech Republic, Austria and Slovenia this summer and so I had the same question as you. I got some advice from Rick Steve's people and decided on the Eurail Pass for Germany, Austria and Slovenia (3 countries for 6 days) The travel in the Czech Republic is supposed to be cheaper than a pass so we are going to purchase tickets directly when we arrive.
I would suggest that you get the Germany-Swiss combo pass and then pay as you go in the Czech Republic. Good luck and have fun!