I’m thinking none of this has to be so complicated. One morning, we walked from the port to the train station (I think a shuttle brought us part of the way), got on the train, got off and walked to the Vatican, did our tour, walked back to the station, took the train back to the port, and walked back to the ship (no shuttle-it was crowded). No train tickets purchased in advance. Yes Vatican tour tickets purchased in advance. First time to Italy. The only research was to determine which train station was closest to the Vatican. Maps on our phones got us to where we needed to be.