All of these sights call for pre-purchased tickets:
Vatican Museums. Online tickets sell out, and the ticket-buying line tends to be long and slow. Expect to be part of a mob. Many folks Iike to buy tickets for the first entry time, which may allow some less-crowded time at the beginning of your visit.
St. Paul's [St. Peter's, of course] with audio guide; that gets you into the shorter/faster security line. There are commercial tours combining the Museums and St. Paul's [St. Peter's], but regular tickets purchased from the Vatican are a lot cheaper.
Borghese Gallery. The gallery limits the number of tickets sold for each 2-hour time block. It's popular and always sold out, but not grossly overcrowded like the Vatican Museums.
Domus Aurea. This is an active archaeological site open Fri-Sun only (I think). Very limited ticket availability; I believe it always sells out.
Colosseum. There are some special tickets that are extremely difficult to get. You can use the Search function here to read about recent experiences.
San Clemente. It doesn't sell out very early, but as of 2023 tickets had to be purchased online; there was no ticket counter at the church.
Not having been to Rome in November (normally a slower month, but it will still be Holy Year), I have no idea how early tickets need to be purchased, except that I don't think you need to worry about San Clemente yet. In general, the earliest time slots tend to sell out first, though I think some folks are a bit reluctant to commit to the 8 AM tickets for the Vatican Museums. It helps that you have a week in Rome, providing some schedule flexibility.