Joyceh, You are correct about the tours. We have done this tour and also the more difficult to book "Scavi" tour..but it was a few years ago and things have changed. You are going to need to directly contact the Vatican via Fax to get the tour and there are no guarantees. The web site with all the info can be found at :
If the direct link does not work copy and paste into your browser. It is very important that you follow the Vatican's instructions exactly as posted on their site.