Excellent decision to take the Scavi tour! I did this tour (pilgrimage as the guide corrected our group - they tend to get particular on that topic) on my trip to Italy last year, and came away fascinated. The wonderfully preserved state of the necropolis that you see at the beginning of the tour really gives you an idea of how ancient Romans remembered their dead. It's very cool, and you'll learn so much.
To clarify some items about the Scavi tour and the Vatican Museums that may help with travel planning... The Scavi tour ends in the grotto under St Peter's Basilica (the grotto is actually the foundation layer of the original medieval St Peter's Basilica). You walk out of that underground area and then have the option to go up the outdoor stairs into St Peter's Basilica proper. The entrance to the Vatican Museums is all the way around the opposite/back side of the basilica. You would need to walk around the perimeter of Vatican City to get to the Museums entrance (approximately 30min walk). As so aptly noted with the hair-raising comment, the crowds are a real crush, especially for the Vatican Museums. They have a very specific traffic flow for the Museum crowds that ends at the basilica. I'm not aware of a way to backtrack.
Decide if the Vatican Museums are a must-see. If so, I recommend a "before they open" tour taken on a different day during your stay in Rome. Otherwise, as mentioned, there are many, many sights and museums of equally memorable value.
Happy planning, I hope you have a wonderful time in Rome!