My goodness Dorothy, we have been to Rome more then 7 times including multi-day stays at various hotels and still could not answer all your questions. We applaud you doing homework, but you don't want to get carried away and over complicated things. The Roma pass does not include the Vatican Museums (Sistine Chapel) and does not appear to cover the train between Civitavecchia and Rome. Unless you plan on spending your day in Museums (not the best way to enjoy Rome) we do not generally recommend the Roma pass for a port day. You will have to leave Rome around mid-afternoon, and if you go to the Vatican that will take more then half your day. We really like the BIRG Pass which covers the round trip regional train from Civitavecchia to Rome plus unlimited use of the Rome metro and bus lines....all for only 9 Euros. You cannot buy the BIRG in advance, or at least it would be foolhardy. You can get it in the Civitavecchia train station at the ticket window or at any of several newstands in and around the station. Make sure you validate the ticket (in the yellow validation machines located near or on the platform) before you get on the first train. We generally suggest folks do the Vatican first (there can be long lines) since its difficult to judge how much time you will need to do the tour. After the Vatican you can better judge what you can do in the remaining time. No reason to get hung up on that last question about the 3 Civ options (have no clue about this) since its a non-issue. There is only one train stop in Civitavecchia for the regional trains and its a 4 block walk from the port entrance where there are free shuttle buses to the ships. Also keep in mind that the real charm of Rome can only be discovered by walking in the city....not using buses and metro for everything.
Since you are obsessive I will try and deal with a few other issues. The FR3 line runs between Rome and Viterbo (a totally different town then Civitavecchia) and is not relevant. The FR5 Line is the designation of the regional line that runs to Civitavecchia, but I doubt if even the Italians know its technically the FR5 and you will probably not see that term posted anywhere. The train that runs between Civitavecchi and Rome does stop at the S. Pietro station (closest to the Vatican) and if you get off at that station on the way into Rome it will save you a lot of time getting to the Vatican rather then going to the Termini station and then taking the metro back to the Vatican.