I would appreciate comments on taking the train to Rome from Civitavecchia and getting to the Vatican museums as a first stop. We are in port until 8pm but I am concerned about lines etc. Is it walkable from the St Peters train stop or should we taxi or metro from Termini. Also, can you get tours once you are at the museum. Thank you

I waited in line for a couple of hours last week to view the Vatican museum. When you get to the back of the line you can figure that for every 100 yards of people it will take 10 minutes to get closer.

Let me offer a way you might save some time. Most of the trains (not all) from "Civ" to Rome stop in several Rome train stations. In fact, the locals often stop at 6 different Rome stations with the last station being the well known main Termini. However, if you get on a train that stops at S. Pietro, this station is very close to St Peters. Another nice thing about getting off at this station is the train will stop there about 23 min before it gets to the Termini. You can actually walk to Vatican and be in line before the train even gets to the Rome Termini. As an example, the 9:02 train from "Civ" arrives at S.Pietro at 9:57 but doesnt get to the Termini station until 10:20. This is a fast stop at S. Pietro so you need to be ready to get off as soon as the train arrives. The 8:02 and 8:41 trains also stop at S. Pietro. The slightly faster ICE and other expresses do not stop at the smaller station. You cannot get a tour at the Vatican Museum unless you make an advance reservation directly with the Vatican. You need to fax them and during the busy summer season you will need some luck to get accepted on a tour. Without a tour its a good idea to have a decent guide book (they sell them at the Vatican). I believe you can also get audio guides.

Hank

Don't bother with the train. There's a wonderful public bus which picks you up at the entrance to the port and drops you right at the Vatican. You can buy a return ticket, not expensive, and it leaves Rome with plenty of time to make your ship's departure. We did this a couple of years ago and we found it to be better than the train

Hank is correct but its quite a hike to the entry of the Museum. You can go up the via Aurelia pretty steep hill (my apt is on it)and walk around the back but part of the way there is no sidewalk, or you can walk past the front of St. Peters through the pillars on the far side down the porta angelica and around to the back where the entry is located.
Best time to go I have found is in the afternoon around 2pm when the tour groups have gone you can usually walk right in with no waiting. Entry closes around 3-3:15pm you have to be out of there by 5pm.
Be sure you get the train schedule its always changing and you don't want to miss a train at St. Pet. only to have to take bus or cab to termini to catch one.

2nd thought. Rome; St. P to Vatcian back to ship if needed or elsewhere in Rome.

If you want a cheap driver the guy who works at our building drives in afternoons.
Great guy, good van, cheap prices. If you interested contact me and I will give you his info.

Call me crazy, but by the time I got to the port I was exhausted from the previous three weeks of travelling. I hired a taxi and paid 100 euros each way to and from my hotel in San Marco. In my opinion, the best money spent so far. No hassle with other people, no trying to figure out what to do with luggage, and definitely the quickest way to San Marco... Less than an hour start to finish.