After getting some advice and help here, we (wife and I) have pulled the trigger and bought our plane tickets (through United) and here is "the plan":
9/29-Depart SFO
9/30-Land Munich, Depart for/arrive in Venice
9/30-10/5 - Venice (staying Dourosouro)
10/5 -Travel via train to Florence and pick up rental car, drive to Noce (between Greve and Certaldo)
10/6-8 - Explore Tuscany (Siena, Volterra, Montepulciano, etc.) using Noce (agriturismo w/ pool) as base (have some concerns about where to eat dinner)
10/9 - Drive back to Florence and drop off the car
10/9-14 - Florence (have bicycles here too, if that will be useful) (staying near Palazzo Medici Riccardi, between train station and Accademia Gallery)
10/14 - Train to Naples and Circumvesuviana on to Sorrento
!0/14-18 - Sorrento (considering renting a car for two days here - use it for Pompeii, Herculaneum one day and Paestum the next)
10/18 - Train to Rome
10/18-24 - Rome (staying near Forum)
10/24 Fly back to San Francisco
Thoughts? Suggestions? Restaurant recommendations? I will probably also be asking some questions on car rental details or train tips at some point, but there we are for now.