divide time in Florence and Tuscan countryside if you can
Ciao Heather,
Sorry I hadn't replied sooner, had somehow missed your additional post.
The area between Siena and Pisa sounds like a good area to stay in, it is also vast so you will have lots of choices in regards to accommodation.
If this is your first time to Tuscany and Florence, then I recommend dividing up your time and spending those 3 days for Florence and the rest in the countryside.. if you've been to Florence before, you might enjoy the time better spending it all in the countryside and taking day trips into Florence, Siena, San Gimignano, Pisa....
You will have a chance to see lots of history, culture, scenery and eat great food wherever you go in Italy (just avoid very touristy restaurants in Rome and Florence).
Are you still considering traveling only by train while in Tuscany or will you rent a car? That will make all the difference in your choices of where to stay - if you don't have a car in Tuscany, you'll have to stay in a town along where you know the train passes so that you can easily move about. Otherwise you will have problems getting into a town and depending only on buses and their schedules.
If you rent a car, you will have more flexibility and the choice of whether or not pick to stay in a farmhouse or villa in the countryside away from a town.
For Rome-Budapest:
You can either fly or take the train - check airfares to see if you get a better deal than taking the train, it saves a lot of travel time. Check
http://www.cheaptickets.com/, for example. I did a quick search and found fares with Alitalia for around $176 per person.
Train - there is only one train per day that leaves Rome to Budapest. It costs around 117 euro per person, traveling second class, and leaves Roma Termini station at 4.50 p.m. with a train change in Venice Mestre and arrive the next day at 11 a.m.
By air sounds much better and cost is almost the same once you convert euros to dollars!