vatican

Barbara, If your Scavi tour starts around 09:00, then it should finish in/near St. Peter's Basilica around 10:30. That gives you plenty of time to tour the Basilica, St. Peter's Square... and then head to lunch! After lunch, perhaps 14:00, you can head over to the Vatican Museums, where you can see the Sistine Chapel... you do have to enter the Museums to see the Sistine Chapel. If you pre-purchase your Vatican Museum tickets, you can "skip" any lines. But you may not need to purchase skip-the-line tickets, depending on which day of week and time of the year you are going to the Museums. Usually by 2 PM on most days there is NO line. Once you enter the museums, you cannot exit and then return. It's a one-time entry fee.

Barbara,
The only thought I would add is if you have time the day before your Scavi tour to see St. Peters, that might be a good idea. Or, keep time flexible the next day............because, sometimes St. Peters will be closed for various reasons (private masses, events, etc.) The first time I was in Rome (on a RS tour), we missed seeing St. Peters because of a private mass (our tour guide inquired and was told the line was 4-hours long once people would be allowed inside), then the second trip we planned it was announced a month after we made our booking that the beatification would be taking place the day before our arrival.....so again, St. Peters was closed even though our Scavi Tour was able to still take place. (Granted, we had many special opportunities, experiences because of the beatification....the crowds were colorful, masses outside, etc. After traveling to other places in Italy, we returned to Rome before flying home and were finally able to get in St. Peters on the third attempt. I have a photo of myself going through the door with a thumbs up.....finally. You really don't want to miss St. Peters....it is fabulous. Also, it's a good idea to tackle the dome first thing in the a.m. right when they open, as it gets really crowded as the day progresses. Another good reason to spread the Vatican over two days, if it works for your schedule. Views from outside on the top of the dome are incredible, and the views from the inside looking down into St. Peters are also great. But, you have the right idea to take it all in from bottom to top....all interesting and wonderful. Enjoy.....safe travels.

I agree with Margaret. We did the Vatican Museum and came back the next day to tour St. Peters. It was just more relaxing that way. When the Vatican Museum is running at full bore, they herd you through the place. It just wasn't as good as it would have been going slower.
Of course, we were there on Good Friday. My best suggestion on visiting Rome is to learn how to negotiate the public transport system, including the subway. It'll help you not walk your legs off.