Derek, Thanks for checking.
Everything went great. Both hotels worked out perfectly.
Would absolutely recommend Borgo Scopeto. It is peaceful, beautiful views, service was excellent and the restaurant is fantastic (we ate there 2 of the nights). It was a great Tuscan experience.
Tour of Vatican was very good and, as you recommended, not something to do on your own.
Transfers and trains all went smoothly.
If you have specific questions or want to talk, feel free to give me a call.
Best, Joe F.