For the 3hr tours, it seems they do the museums, then chapel, then basilica. I was told they have special permission (skip line) into st.peter's, but leaving early means potentially missing that. So now it's between 2pm guided tour, or just 2-2:30 entry quick self-tour (likely missing out on basilica), or saving vatican for next time.
To clarify, this day is mid-cruise so we'll be going into Rome in the morning w/o luggage. We're trying to squeeze in coloseum midday and decided to go there first because it's more flexible on time since we can hang around the forum next door first before 11am timed entry (whereas if we schedule 10am vatican and get there late we might well miss out on entire tour).
Having never been there, the connection back to the ship seems confusing with many stages and different options (like 3 different ways to get to the ship even after getting off train). Cruise advises getting on at least 30m prior (7:30).
Yes I know it's a squeeze trying to see the city and vatican on the same day, I'm just scheduling the hours and seeing what works or not. Thanks for all the advice.