I took the VFR tour with two other family members in 2023. At the time, the Vatican Museum & Sistine Chapel were included, so I can't speak to booking that separately. We did go to St. Mark's and the Doge's Palace on our own the morning before the first tour group meeting. We were there in March of that year, so we didn't buy our tickets until that day.
I took the Alilaguna from the airport to Venice--I found the directions provided in the pre-tour packet on how to get to the first hotel easy to follow.
Advice? Do a lot of walking/stair climbing at home to prep for the trip. When there, give yourself time to sit and have a spritz or a cup of coffee in one of the little campos away from the crowd every now and then, and soak it all in. The wine tasting lunch near Orvieto, Umbria, was one of my favorite activities on the tour, and in the cities, I loved the backstreets walking tours, especially in Florence because the centre was quite crowded, more so than Venice and Rome, I thought. We also had a fun cooking class while in Florence.
We spent a night and day in Assisi post tour, and that was also a great memory.
Great tour! Hope you really enjoy!