NO. They do NOT stamp your passport at all, you will be issued with a separate paper visa
Shekels is the currency used, you are advised to exchange your money locally, once you have arrived in Jerusalem.
If you are not able to attend the full duration of the trip but wish to come in between the trip, the same fee would still apply.
You are required to book the set flights which the group will be traveling on. If however, you decide to book alternative flights, you would be required to make your own way to and from the hotel.