If we were to purchase tickets and reservations for the vatican (without a tour guide)----can you start anywhere in the museum(s)--taking your time in each area? Or do you have to follow a set movement from place to place as you're "herded" through the museum(s)---same for Sistine Chapel--can you take your time in there if you're on your own?
It will be a little difficult to start "anywhere" since they do start you out at a point and cordon the areas to direct traffic. But yes, you can linger as long as you like in any area.
If you want to visit the Pinacoteca, Gregorian Profane, Pio-Christian, Missionary-Ethnological and/or Carriage Museums, it's good to see them before entering the main galleries, instead of having to backtrack. I visited the first 3 and enjoyed them very much.
You can take your time, but keep in mind that the collections are huge, so pace yourselves to spend enough time at the places that most interest you.
There are very few "shortcuts" between sections, so you pretty much have to go with the flow, and you will walk through most of the galleries, but you don't have to linger.