Alps: You don't have a whole lot of time (just 2 weeks), therefore you should concentrate only one one portion of the Alps, either the Val D'Aosta (e.g. Courmayeur) or the Dolomites (Val Gardena is my favorite), but not both because they are quite a distance from each other and you'll be spending a lot of time driving from one to the other. You can also combine a visit to a lake while you are in the area. Lake Garda is next to the Dolomites and Lake Maggiore is near the Val D'Aosta. Since you eventually plan to go to Venice, I would choose the Dolomites/Lake Garda area because it's very close to Venice, whereas the Val D'Aosta is quite a drive to Venice.
Although everything in Italy is doable with public transport, however the Alpine region is better done by car because you can cover more territory with a car and some spots in the mountains have less frequent bus service.
You should return the rental car the minute you arrive in Venice. You won't really need a car for the rest of your itinerary.
I don't think you need 3 nights in Siena unless you use it as a base to also visit some of the small hilltowns in the area.
Even if you don't enjoy crowds and big cities, however the last 2 nights are appropriately allocated to Florence. If you fly back from Florence you need to spend the last night there anyhow (flights are probably very early morning to get back to North America via some EU hubs). So you might as well add one night and have at least a full day for sightseeing and maybe some last minute shopping.
I think the Ferrari factory tour is open only to Ferrari car owners. If you don't own a Ferrari you can visit the Museum or you can buy a Ferrari just before going to Italy. The Ferrari factory is in Maranello, a suburb of Modena.
