We took the train from the port to St.Peters, wandered around there for a while and then walked to the Vatican. There was no way we were getting into the Basilica. The line was hours long. I had tried to get skip-the-line tickets prior, but none were available, even though I checked months before the trip.
We had booked our Vatican tour through the official Vatican sight, again months before. It is clear on the website when the ticket blocks are released. It was a three-hour tour (I’m now humming the Gilligan’s Island theme song. Are you?), which ended in the Sistine Chapel. We then walked back to the train and were back on board the ship in plenty of time. The whole trip did take about 8 hours, but we did have coffee in the morning and a nice lunch. We were in port about 12 hours.
However, 8 hours doesn’t leave any margin of error. I’d look for a shorter Vatican tour. Maybe there’s one that covers both in a shorter time period? The train was actually a very efficient mode of travel. Less than an hour each way. We just took regular commuter trains.