renting a car/driving/train advice

I'd consider getting the car in La Spezia and dropping it in Florence. A GPS will help if you are familiar with using one (or a smartphone with an Italian sim card). You won't save money buying train tickets now so you may as well leave times open and buy them as you go. Look up what a ZTL sign looks like and don't drive into a small town that has them (including Florence). Parking outside the walls is usually the safe way to avoid expensive tickets that arrive after you get home.

I really enjoyed touring Tuscany and Chianti by car and look forward to doing it again.

1) Where is the best site to reserve train tickets/do we really need to reserve them or better off getting them there? Need to get reserved times?
You can potentially save big $$$ by booking trains ahead. http://www.trenitalia.com/tcom-en

2) We are planning on renting car for the Montepulciano portion between Cinque Terre and Florence (for 2 days). Where to pick up/drop off rental car? Where to reserve from? Already got my International Drivers Permit!
La Spezia / Florence

3) Any recommendations for what to do during our 2 days in Montepulciano? I saw Rick Steves has a driving loop we can do around some of the towns, but always looking for more rec's. Would like to keep this portion of our trip a little more laid back and relaxing, so winery tours are definitely an option!
Siena / San Gimignano / Chianti drive
Lucca from La Spezia

If you are suggesting San Gimignano, you might look at a Rick Steves video blog from last week when he condemned it as no more than a tourist trap.

Conveniently forgetting that it was he who sent millions there when he called it the best hill town in Italy.

San Gimignano is the most beautiful quintessentially medieval hill town in Tuscany and it should be a must for anybody that has never visited it before, I don't care how touristy it gets and I don't care how Rick Steves describes it.

If one had to avoid touristy places in Italy, one should avoid also the Cinque Terre, Florence and Venice, all of which get far more tourists than San Gimignano.

There is a reason why Venice gets more crowded with tourists than Porto Marghera.

Thank you! This is all such great information!

Rallytay,
When visiting very popular towns like Siena, San Gimignano, and Assisi, especially during busy months May through October, try to avoid the heart of the day, like 11 am to 4 pm, when everybody else is there for the day, including bus loads. Try to be there early morning and/or late afternoon and evening. Spending one or better two nights in these towns is best, maybe taking a day trip from there to a less popular area.
With car rentals, make sure EACH driver has an IDP just in case you are stopped or have some kind of accident. Also, make sure you know how to get into reverse before you drive away from the rental office. That is problem I experienced, with a brand new car with a simple but somewhat new (to me) way to get into reverse that I could not figure out on my own.
On winery explorations, always an excellent idea to have a designated driver!

If your trip is two weeks from now, you may not really save big $$$ by booking train tickets now, although you could still get some discounts, primarily on your first and last (longer) trips of the itinerary above. Don't book a train unless you are ready to commit. They are not likely to sell out and even full fare is a fairly reasonable price.

I think you were also asking which car rental company to use. We have used Auto Europe so many times that I have lost track, and have always had a good experience. Easy to change things, too. They are a consolidator.

I love San Gimignano, but primarily because we have stayed IN this small city a number of times, and do day trips from there. So we are rarely there when the multitude of tourists are, but instead, are there in the evening when it's quiet and peaceful to sit in the main square with a glass of wine. Or take a walk around the city walls in the early morning, when few others are about.

The Chianti towns may be further than you want to go with the amount of time that you have. If you like Brunellos, then definitely head down to Montalcino. The biggest winery, and the one that I thought was the most like those in California, is Castello Banfi. Check to see if you need to make reservations in advance for a tour. It's been a long time since we visited wineries in Tuscany, but in general, its different than touring wineries in the U.S. Mostly you need to make reservations. Ask your hotel to help you out with that.

Enjoy!