Transportation – Ah, another one that is quite subjective to the mode and time of year you go. For basic economy flights from a gateway location I would expect to see $1200-$1800 per person. If you see under $1000 (including tax), then you are winning in my opinion!
For the mode of transportation between the cities, I highly recommend the train. Parking in the cities is a nightmare to an American, and you normally have to pay per day to park it (even at your hotel, if they offer parking). When you are in the city, the easiest way to get around is walking or public transport.
We made the mistake of renting a car and then parking it on the outskirts of town for the first 3 days we were in Venice. There went a couple of hundreds dollars wasted. So if you do rent a car, pick it up on the way out of town!
If you decide the train is the best way to go, then buy your tickets ahead of time, they are pretty cheap! For example, you can get a ticket from Venice to Florence for about $20 per person.