If possible, fly open-jaw, into Venice and out of Rome. That will save you backtracking and it's easy to fly out of Rome than out of Venice. Also, Venice is a great place to relax and soak up the atmosphere while you get over the jetlag.
In Venice, you will want to have Shabbat dinner at GamGam Restaurant, hosted by Chabad and very lively, always lots of singing, an interesting "d'rash" and very good Israeli-style food. It's usually packed. In the morning, go to the Sephardi/Italian minyan, not Chabad. There are 2 major synagogues in the Ghetto, I was told they alternate (same minyan). That will give you more opportunity to mix with the locals, though Chabad's services do start later in the morning. When I was there a few years ago, they had an overloaded buffet for kiddush and was told that's a regular thing. If you're still hungry, you can walk over to GamGam for lunch, hosted by Chabad. Take the synagogue tour in Venice, very interesting. The museum wasn't much though. You don't have to stay in/near the Ghetto - it's not a very long walk there or to GamGam from anywhere in the city.
The Great Synagogue in Florence is beautiful . . . and huge. Pisa may be easier as a 1/2 day trip from Florence. Then you can take the train to the closer Pisa Rossore station. If you have luggage, you'll need to store it at Pisa Centrale station. People recommend combining Pisa and Lucca in one day trip. It is possible to enjoy the CT in a one-night stay. The trick is to get a convenient train between the CT and Rome. Get there as early as possible and have some time before dark to explore. Spend most of the next day hiking part of the main trail. Fit in an afternoon ferry ride when you arrive or before you leave - some of the best views are from the sea in the mid to late afternoon sun. Evening train to your next destination.
In Rome, Micaela Pavoncello always gets high marks for her Jewish tours. There are kosher restaurants in the tiny Ghetto (about 1 block long) but be careful - not all of them are kosher. You may be interested in staying here (kosher and Shabbat facilities). Consider a day trip to Ostia Antica, besides being a very interesting archaeological site (download Rick's audio tour), there's a synagogue.
