Hello,
We absolutely loved our visit to Vatican, and we are glad that we made the trip.
To answer your question, here are a few things I think could be helpful (please note that my experience is limited; we visited Vatican just once, and without a tour guide):
- Vatican is massive indeed, and it is exhausting to visit Vatican, both physically (long walks, stairs, having to look up until your neck hurts, etc.) and mentally (so many things to look at, people not being so courteous, etc.).
- Sistine Chapel - You will be looking up at the ceiling for some time. I think Rick Steves' audio tour of Sistine is about 30 minutes long.
- The line to get into St. Peter's Basilica is very long, unless you get there very early. I do not know much about skip-the-line deals with tour groups, but I saw some tour groups stuck in the line for very long time.
That being said, I personally think it would be more feasible to get separate tickets and visit St. Peter's later (get food in between!). Also, for most tour groups, I think they wouldn't allow too much time for shopping at museum stores, since they have spots to hit and come back for the next tour. Maybe private tour guides can accommodate your plan?
Hope this helped.