Hi Gogetter. We have booked train tickets over the internet on the Trenitalia website. Tickets don't become available for reservation until 30 days prior to your departure date. We checked this out with a travel agent who also confirmed this is how Trenitalia works.
You can prebook Vatican Museum tours by going to www.vatican.va
and searching under museum, guided tours. The instructions are all there. You need to fax the Vatican a minimum of 1 week, preferably 1 month, before arriving and give them your preferred dates and times. They will fax you back a tour confirmation which you have 7 days to pay for. Then take the confirmation fax to a separate line up at the Vatican Museum 15 minutes before your tour time and you're in!
Have fun on your cruise!