Thanks everyone for all of the help and suggestions! We had a great trip. We tried to do something sort of "big-ish" everyday and then just walked around exploring and experiencing the area and eating gelato the rest of the day. We generally were out quite late, particularly in Rome. Here's a rough rundown of what we ended up doing:
Day 1: arrived in Rome in the afternoon, checked into the apartment, rested a bit, then walked around the surrounding neighborhood around the Campo de Fiori and along the Tiber River.
Day 2: tour of the Colosseum and the Roman Forum. In the evening we walked from our apartment to Campo de Fiori, Piazza Navone, the Pantheon, Trevi Fountain, and Spanish steps.
Day 3: St. Peter's Basilica and climbed up the dome. More walking around. Went inside the Pantheon in the day and the Trevi Fountain again.
Day 4: Priscilla Catacombs. Spent some time in Villa Borghese and rented one of those electric double bike things to ride around. We walked by the cat sancutary - it was closed at this point but we still got to cat-watch. At night we walked to a restaurant in the neighborhood of Trastavere where my husband's mom ate at 50 years ago.
Day 5: train to Pisa. Checked into hotel and walked to the Field of Miracles. My son and husband climbed the stairs in the leaning tower, while my daughter and I sat outside, planning her birthday party. We went in the the Cathedral. We went for dinner and went back to the Field of Miracles at night where the kids had fun running around there.
Day 6: This was our most exhausting day. We took the train to Venice. We had to stop by an office to get the keys to our apartment and finding it was hard - also finding the apartment was hard. Once there, we walked around a bit in Venice and to St. Mark's square. The kids enjoyed chasing pigeons.
Day 7: We did a rowing lesson with Row Venice. It was really fun, partly because it was in a different neighborhood from where the usual tourists go, so it was much more quiet. My son really enjoyed rowing. We also took the elevator up the Campanile in the early evening.
Day 8: We went to Murano and Burano. Spent the rest of the day and evening walking around Venice. My son picked out a journal, covered with Venice marbled paper and sketched some pigeons and the Campanile.
Day 9: headed home!
The kids really had a great time and loved just walking around, eating gelato, and exploring!