i have reservations for the scavi tour in feburary at 9:15 am...questions...do i have to go through security before hand and how much before my appointment should i be there to go through the whole process? also, can i get into st.peter's basilica after or do i have to get into another line?
There is no line that you need to wait in assuming that you are not carrying a large bag. If you are carrying a bag then you will need to check the bag first and I believe that means going through security. I had only a small purse and I was not required to check it.
Your reservation confirmation should have instructions. Make sure to bring a copy of your email reservation. When I went (2 years ago ... check your letter in case things have changed), I showed the email to the Swiss Guard and they let me pass the barrier to go back to the Scavi Office. The entrance was on the left side of St Peters (as you face the Basilica).
My tour ended in the grotto beneath St Peters (where popes are buried). I did not go into the Basilica after the tour, so I do not know if you can avoid the line.