Ciao Soo, seems like a very good itinerary so far! I really like the idea of having your base near San Gimignano and from there doing day trips and taking some time to take it easy and explore the area slowly :-)
One suggestion I'd make is this: return the car rental once you return to Florence as you don't need a car in the historical part of town (unless you're in the outskirts and have parking included). You won't be able to drive it in the historical area, will need to have it parked those last few days and it is around 20-30 euros per day of parking - so if you're central, return the car and your last day catch the bus shuttle from SMN to the airport or call a cab (especially if you're catching an early flight).
As far as car rentals go, there are automatic transmissions but since they aren't as commonly used here, their cost is higher than the manuals --- so scroll through the entire list of results, you'll see they tend to be at the bottom since the list is organized by price. The search with rentalcars.com is pretty good since it searches through all of the major agencies (Hertz, Avis, Europcar, etc.).
As for tolls between Florence, Siena, San Gimignano - luckily for now, the Firenze-Siena road that connects all of these places is still toll-free! As are the regional roads off of this one, so no tolls for youOnly the A11, A1, A12 have tolls, the Florence-Pisa-Livorno is also toll-free.
For accommodation, start by taking a look here http://www.tuscanyaccommodation.com/
You can navigate the maps to find places around San Gimignano or that general area in any case.
For Florence - if you return the car when you return to town, you'll have more options.... but if you want one with parking, start from this list:
http://www.florenceaccommodation.com...-with-parking/
I'd recommend Hotel Principe and Apartment Guelfa as both are in the center, then head outwards...
Hope I've answered most of your questions, if I missed something or have more questions, let me know!
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