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.