We did the Jewish quarter during our free time. You can buy the tickets to all 4 sites. We were so glad that we saw it! We did not get to Prague early :( but there is so much to see and do. You will do the castle complex with your group and a guide, and will be released at that point so you can go back and look at more if you want to. The Communist museum is great, if you are interested in communist history. (it was created by an american.)
I will tell you that if you are interested in Communism history then you should book the tour of Nowa Huta District early (Krakow Communism tour) One of our tour members really wanted to do that and they were pretty booked. She had to miss our tour activity in order to go. http://www.crazyguides.com Had we had more time in Krakow I would have done that tour as well. But we are Catholic and there is so much to see in Krakow, that we didn't have time. When we go back we will do it.
We did do the Underground Museum in Krakow (it is under the market hall) It is an excavation sight of the old market hall. If you are into archeology, or how they used to live you should consider doing it. You can buy the tickets at the TI on the square and you can skip the line and are guaranteed in. We were amazed by the museum, because it is all excavated, so you feel like you are in the 1500's again.
Please feel free to contact me with any questions. We had a great time, but I, like you had a hard time finding information about the tour from previous tour members.