2 Weeks Itinerary

It's not a good idea to spend your last night in Florence when you're flying home from Milan. Is your home in North America? You'll need to be at the airport at least 3 hours before the flight, which is 9:30 AM. Whether you're taking the train (as in your case) or driving, it's always possible for something to go wrong, so my policy is to spend my last night in a place that's an affordable taxi ride from the airport, just in case.

In your situation, flying home on a Sunday, you will have to take the 1:07 AM train from Florence in order to get to Malpensa by 9:30 AM. The first fast train (Freccia) doesn't leave Florence until 7:55 AM and reaches Milano Centrale at 9:50. Malpensa Airport is a long train ride from Milano Centrale, plus you have to factor in the connection/layover time. It just will not work.

I'd choose Venice over the Cinque Terre, but that doesn't mean you have to. I consider Venice a 3-night city at a minimum. If you try to rush it, you'll end up spending way too much of your time in a tourist scrum, seeing the same places all the day-trippers want to see. You need time in Venice to get into the back canals and forgotten corners.

1. It would take years to see it all, so just make a list of what you want to see this time. It's a solid allotment of time knowing nothing else.
2. AC and CT have differences, but a basic similarity--both are coastal beauty spots where the main activities are chilling, enjoying the view, hiking. I don't see any reason to include both for that reason, as you can enjoy the beauty, relax, and hike on the Amalfi Coast (where I found it easier to escape the crowds, given that it is a much larger area). I would certainly look at the travel time involved in getting from one to the other--that is going to be a long travel day no matter what. I would actually consider going to the Amalfi Coast first, even though it involves some backtracking, so you can then travel north--Rome then Florence. Or, just add the two CT days to the AC and visit Pompeii while there.

Hard to say if you should exclude CT or AC. I have been to both and enjoyed them both. I saw CT on one trip when we traveled Venice to Rome and in between. Saw AC when we traveled Naples to AC to Puglia. One way to decide is if you can get accommodations. Both areas fill up quickly and finding a place to stay that meet your needs at this point may not be so easy.

Seeing Pompeii and Pisa is again, a personal choice. Not for me to say. I saw both and was glad I did. That's me. Others would say skip Pisa ( I'm assuming you want to visit the leaning tower and Piazza dei Miracoli) You need to visit what interest you and your family.