Jenny, for more info on the Roma Pass, CLICK HERE . There will be no Papal Audiences in Rome in September (although some are shown on the Vatican website, the Vatican is saying that these will be done at the Pope's "retreat" as he does not usually return to Rome until October).
The Vatican Museums ticket DOES include the Sistine Chapel. The Vatican Gardens ( which I think are over-rated for the cost) are a separate ticket. The primary section of St. Peter's Basilica is FREE, and so are the Pope's tombs downstairs, although you will pay to climb to the top of the cupola (or ride the elevator) and there is a charge if you want to go into the Museum "wing" of the Basilica.
I think you will have no problems, especially in the afternoon, avoiding lines in September. It's all about timing! For more info on avoiding lines at the Vatican, CLICK HERE