I am pretty new here, but I was just recently in Rome for 10 days. The vatican is definately worth visiting. The Scavi Tour is tour of the ongoing excavations beneath the vatican. There you can see the tomb of st. Peter. You need to reserve well in advance, because they only allow 200 visitors a day in the necropolis. Unfortunately I sent my request too late, so I cant tell you about the tour, but it sounds interesting.
To apply you need to send an email to firstname.lastname@example.org
and tell them the number of people in your group and the date you want to visit. The cost is 10 Euros per person.
I hope you get lucky.