Susan, first off, my wife and I are probably crazy for trying to attempt this. Time-wise, it works out, but we certainly won't be enjoying a relaxing walk through Florence. We will be zipping from site to site. Most people wouldn't want to do this, but we are willing to give it a shot.
Why? Because our ship stops at Livorno on a Monday, which means the Uffizi and Accademia are closed. Originally, we were going to do the very same Florence and Pisa tour you spoke of, and I agree...it's just not good enough. At the same time, I REALLY want to see Siena and San Gimignano, and we couldn't do all four things in one stop.
So, here is our current plan. Get up early in Rome on Day 4 (ship departs on Day 5), take the Metro to Termini station, catch the 6:30 AM train (the fast one, a bit more expensive) that arrives in Florence at 8:09 AM. Then, with reservations in place for the museums, we go to the Accademia (spend max of one hour there) and Uffizi (max of two hours there), we briefly see the Ponte Vecchio, we MAYBE swing by Santa Croce (only if time allows), we see the Duomo and Baptistry (entering or not entering depending on lines), and that's about it. Lunch would be a quick to go panino, and maybe a gelato.
We try to get out of Florence by around 3:30, and take a 1 hour 15 minute train to Pisa. After we get off the train we catch the 15 min bus to the Field of Miracles, then we have about an hour and a half there. I don't see us needing more, based on what I've heard about Pisa. It's something to say you've seen, and little more, according to a large number of people. So, then we catch the 7 PM train out of Pisa to Rome, which is a 3-4 hour trip. I assume we'll sleep on the train.
So there you have it... Our crazy plan!