Shraga, I would suggest you divide your activities by location. In addition to the Kosel tunnels, there are other museums in the Jewish quarter, including seeing sites from the times of 2nd BHM’K and also the museum with the keilim from the BHM”K. Lots to see and do in the Old City. Combine that with a visit to the kosel for daavening, eating pizza or whatever else you might like at one of the restaurants, and you will have exhausted a large part of the day, especially with just walking up all of the stairs from the Kosel to the Jewish Quarter.
Other museums can be done on the second day – Yad Vashem will take a couple of hours, and you can get there going on the new Light Rail train just to see some sights, the Israel Museum if that interests you, Science Museum, which you mentioned, a trip to Geulah/Meah Shearim to shop a little and get every one a token to remember their trip with and bring back presents when they go home.
Enjoy your stay.