I have a Scavi Tour at 11AM and although I'd like to do the 3 or 4 hour tour of the Vatican Museums, I don't know if all that is just too much. I really want to see the Sistine Chapel, so is there an audio tour that I can set my own pace and go through quicker than the long tour? I only have this one day to see the Vatican area and waiting to see if the Vatican even answers my request until the day before seems unsettling. Thanks.

You won't be able to do the Sistine Chapel *before* the Scavi tour. The lines are just too long

Afternoon is actually the best time to time your museum entry. If all you want to do is see the Sistine Chapel, you can buy your ticket, wade your way through the crowds, and stand and admire it for as long as you want...

Then, you can exit right directly into St. Peter's and avoid that queue.

You'll be done with the Scavi tour in time to get to the Vatican Museums door at 12:30. Little or no lines at that time.
We took the Scavi tour at 11 and did the same.
You probably would have checked items at St. Peter's before your tour. You can get permission (Swiss guard) to go up the side stairs of St. Peter's (just after you walk out of the Vatican).You might elect to leave them their since you will need to check them again at the museums.
The audio tour is actually quite good and allows you to see what you want at your own speed.
I also recommend at least the "free" (tips allowed) St. Peter's tour. Do this before your Scavi tour.

Thanks a lot. Is there a long line to get the audio or St. Peter's free tour? They are not pre-booked, correct?

No long line for the audio tour at the Vatican...at least not when I was there (first of August). You do have to leave a photo id to ensure the return of the audio.

It sometimes takes a little time returning the machines,but the renting process is quick.