For Jerusalem:
Take either the one or three bus from the tachana to the Kosel.
Daven there.
Go to the Rova
There is also a museum in the rova under Yeshivat HaKotel- its pretty interesting.
There is also another museum in the rova as well.
Eat lunch in the Rova.
Daven Mincha if it is time to do so at the Kosel.
Go back to the tachana Hamerkazit.
Take the 25 to Neve Yaakov.
Get off in Geula.
Spend some time looking at the stores, this is a good time to go to manny’s and get seforim…
Go to Ki Tov for popcorn- its the one with the bags hanging from the ceiling of the store, its a ton of popcorn for a great price (they have other things to, but I only go for the popcorn).
Take the 25 to Machane Yehuda (aka the Shuk) and have try to bargain for lower prices on items such as sunflower seeds (a very popular food in Israel. Make sure you know how to eat them. First you put half the shell in between your teeth so that the narrower ends are vertical, then make three bites on the shell, at the beginning, middle and end, then bite down and remove shell from mouth and eat the seed).
Then take the train to Jaffa Center (Ben Yehuda) and look at the stores. Go to Big Apple Pizza for dinner. There is (if you are not fleishig) this place called Kotzefet, and it has a ton of good treats there, like Ice Cream, Iced Coffee, and smoothies, and frozen yogurt, try some of that) for dessert.
That is all of the ideas I have for a day in Jerusalem in the winter (as long as it is not raining when you are here, it should not be a problem to do all of these things). You can split these plans between tuesday and wednesday, like everything from geula till the end of this itinerary for Jerusalem can be on wednesday.
If that is the case, then from Ben Yehuda, take either the four or 18 to Malcha mall and look at some stores there. Then take the 35 bus to the tachana hamerkazit so that you can go to the next city on your list of places to visit.