Keep in mind that I am pulling from my memory and it's getting hazy.

Regarding Siena, one visit we stayed in a convent in the medieval center which I highly recommend. It was built into the hillside and had very good heat (December), comfort and location. Try for a room facing out overlooking the valley. Another time we stayed at the Jolly Hotel and had a very nice room looking out over the soccer stadium. My food memory in Siena was also at the Jolly. Dinner was included and had lots of waiters and courses. We were determined to try them all and were so full we barely made it up to our room.

Siena has the magnificent zebra stripped duomo, shell shaped piazza, colorful, historic museums of much interest to me, winding and hilly medieval streets. There was a market easily located on certain days of the week and I remember the flowers were beautiful. Also, a huge enoteca located inside/beneath the old fortress which is nice for a stroll and sampling. The well preserved the head of St. Catherine displayed in her reverence was amazing.

We bussed to SanGimangano and saw lots of towers but also lots of tourists.

Near Bagnoregio that Antonio suggested above, I remember the beautiful, colorfully fronted duomo in Orvieto and it was very unique. There was a good gelato place right nearby. I think there was an interesting Etruscan museum in Orvieto and an ancient round stairwell of some sort.

There was a little town outside of Orvieto built on top of a very rocky mountain. You could see it from far off and there looked to be only a suspension-type bridge access going up to it. We parked out on the highway at a rest area and walked up there via the suspension/rope bridge. I don't recall the name of the village on the hilltop but think it had been purchased by a wealthy Italian family who kept a home there.

By the way, I loved Pisa and the people there were friendly. You will be fortunate to go up into the tower now that it is reopened and stabilized. Try to find that local food cici, made of garbanzo beans. That was the only place I ever saw it.

Hope this helps.