Have to agree with Donna on this one. If I were you, Sam, I'd try to find other folks on here looking for similar excursions, in order to set up a guide ahead of time. Speaking from personal experience, Italian cabbies LOVE to prey on silly American tourist, whom they view as an easy source of quick cash. For example, I once once needed a lift from Da Vinci airport (Rome) to a hotel I'd booked, about 3 miles away. At first I didn't realize the taxi had a shuttle, and hopped in the Taxi queue outside. As soon as they guy told me it'd be the llira (before the Euro) equivalent of $75, I nearly gagged, then immediately called the hotel.....
As for the excursions themselves, I'd have to agree again with Donna on Naples. It's easy to find transportation directly from the harbor, as the boat will pull in to the downtown area. My advice is (which ever means of transport you use) get out of town as quickly as possible....
. Nothing against Neapolitans, but it's a big, dirty, crime infested city, and you're better off not wasting time there. The wife and I opted for a cruise line excursion which took us on a drive of the Amalfi coast (Fantastic) and Pompeii. It was a full day, and came with the tourguide, so it was worth the expense. You can do it cheaper (as Donna alluded to) by taking the train out of Naples to the stop for Pompeii.....short ride, only like 15 miles. We didn't make it to Sorrento, but I heard good things about it, as well. Take the fast ferry (hovercraft?) over to save time.
For Rome, we again opted for the cruise excursion.....mainly due to the distance. I'd been to Rome several times in the past, but it was the first time for my wife. Hence, we took the 1/2 day guided tour combined with a 1/2 day to wander as we saw fit. You can NEVER hope to see everything in a day, but I'd have about 4 or 5 things you DEFINITELY want to see, and plan out an order of progression. Note: make sure to bring some form of long pants if you want to get into the vatican, St Peters, or any of the other Churchs. The Italians are sticklers about clothing "propriety", and you won't get in wearing shorts (even in the 100 degree weather we faced).
For Livorno, we took the ships excursion to Florence, which again gave us 1/2 day guided and 1/2 day on our own. Again, I'd already been, so the guided portion was mainly for the wife. We know several folks who opted to hop the train over to Florence, and they made out fine (even getting to see Pisa as well). My opinion on the matter is not to waste time in Pisa (particularly as part of a tour). It's literally a 20 minute stop, you gawk at the leaning tower, and they you're on to Florence anyway. Once you're in Florence, it's VERY easy to get around, as all the the main sites are located in/around the city center (which is very compact). A guide is nice, for little nuances/details, but you can certainly manage on your own (as I did the first time). Make sure to check out the Ponte Vecchia, the Galleria, the Duomo (cathederal) with the Golden Baptistry doors, etc. It was one of my FAVORITE cities in Italy.
Hope this helps, a bit at least.....;-) Have a great time, and best of luck with your transportation issues