About 2.5 months ago I put in a request for my wife and I to take the Scavi tour at St. Peters. I received the autoreply right after I sent in my email.
But since then I have not heard anything.
We are leaving for Rome in 2 weeks, am I basically out of luck since they didn’t confirm the reservation? If I were to follow back up with them; what would be the best way to do so?

There are some good posts about Scavi here. If you do a search, I think you will find the answer to your question ( I remember seeing an answer..)

You can check at the offices on site when you first arrive, but this does involve two visits to St. Peters and on a strict time-budget, that can be a drag. Others have noted on this forum that the Scavi folks are often very slow to confirm but you may find they have put it through on your credit card. In that case you are good to go!

I've heard mostly that they were quick to respond. I think it took us about 2 weeks to hear back. Did you get the inital email saying that a confirmation would follow?

< Did you get the inital email saying that a confirmation would follow? >

Yes I did. But it’s been about two and a half months since then. I’m beginning to think that we weren’t able to get the reservation.
Other than emailing them back again I’m not sure what else can be done.

I would reply to them, with the email they sent to you attached, and ask.