Finalizing Itinerary

My thoughts: CT takes much longer to get to from Florence than does Siena. Do three nights in Venice. Don't stay in Naples proper. Stay in Sorrento. 95% of tourists prefer Sorrento over Naples for very good reasons. I never stay anywhere for less than two nights unless it's a layover. But bigger picture, I would leave Naples/Sorrento/Amalfi off the itinerary all together. Don't go south of Rome on this trip. Take your Naples days and spend them in CT and Siena both. I would suggest this order: Venice Florence Rome (daytrip to Ostia Antica as your Pompeii alternative) Siena CT
Milan to fly home Just my thoughts of course. Everyone has different interests. One more comment - you're going to have more of a challenge finding lodging because this trip is coming up so soon. You'll be able to find it, but you may have to settle for your third, fourth, or fifth choice. Happy travels.

For your question #2, I would stay that extra night in Florence, and take a day trip to Siena. The CT is worth more than just a partial day - by the time you get there, get checked in, etc., you won't have time to enjoy it. One-night stays in a city aren't really fun, so instead of spending the night in Siena, just take the bus there for the day.

CK:
Michael has some very good advice. I like his routing, and the idea to stay Rome and north. It is so tempting to try and see everything, but like a good banquet, you can't put everything on your plate the first time through! By all means stay in Venice at least 3 nights. Truly worth it and a good place to get over jetlag. Skip the Amalfi Coast/Naples/Pompeii this time if you are determined to see the Cinque Terre. Add a 2nd night to the CT, add a night to Rome, add a night to Florence and daytrip to Siena if you must see that city. 5 nights in Rome may give you enough time to do the (very) long daytrip to Pompeii if your heart is set on it. And yes, you can stop in Orvieto on your way to Rome. It's easy enough to stop, ride the funicular, see the Duomo, have lunch, and continue on to Rome.

I'd drop Milan and fly back from Rome. Of all the destinations, Milan is the least interesting. Rome is just over an hour by train from Naples. Milan is another 4 hours.

Okay, I missed your previous draft itineraries. Assuming your flights are booked, here's another thought. Instead of going to Naples to see Pompeii, stay in Rome and take a day trip to Ostia Antica. That will also allow you another full day in Rome (it's 3.50 hours by train to Milan), and you can add a day to Venice and a day to CT or Florence (Siena is a day trip from Florence). If you are still interested in Bologna, you can take an early train out of Venice, leave your luggage at the train station, spend the day in Bologna, and then a late train on to Florence. I did that (but Padua, not Bologna). You can also spend a half day in Pisa on the way from Florence to CT.

I agree, don't go to Naples. If you look at your itinerary, you are traveling 7 days out of a 2 week trip! That really does not leave time for both relaxing and seeing anything. I would suggest what other posters have said, 3 nights Venice-3 nights Florence-2 nights Siena-4 nights Rome-2 nights CT- 2 nights Milan. Even that trip includes over 15 hours of combined train/bus time on the fast trains, not counting checking in and out and waiting for trains. Save Orvieto for another time. Enjoy your trip!