Kyle, I have been to a few of your ports of call
Rome: I used a private company called romeinlimo. I used them for both rome and florence/pisa. They were great, saw more in those two ports than the other ports. In Rome they took us to Colissium, Pantheon, Spanish Steps, Trevi Fountain, and Vatican. Private tour in Colissium and private tour with guide at the vatican.
Florence/Pisa: Used same company as above, They were able to drop us off right next to the Leaning tower; gave us time to sightsee then on to Florence. Florence is about an 1 1/2 hours from port, so u need to consider this on any tour u take.
Dubrovnik; Take the ship shuttle bus. go to downtown Durbrovnik, it is a walled city; great place and lots to see; you can spend a few hours inside the city (it is surrounded by a rock wall), shopping, sightseeing, and places to eat.
Cofu: I visited a Greek Monestary where they pressed their own olive oil; and Achellion Palace (no big deal)
Santorini; the ship will dock in the town of Fira; A must see town is Oia, you can take a taxi there or the city bus. It is about 30 minutes from the port
Kudiashi: My favorite port; This is where u can go to Ephasus, the town where the Apostle Paul taught to the Ephessians for three years; lots of ancient architecture all over. It is about 20 minutes from the port
Hope this helps
Freedom of the Seas Dec 11
Allure of the Seas: Jan 11
Voyager of the Seas: May 09
Splendour of the Seas: May 07
Explorer of the Seas: Jan 04
Majesty of the Seas Jan 99