Ciao Sophie, welcome to our forum!
6 weeks in Italy sounds magnificent! How much have you already "fixed" so far that cannot be changed? You already have a very good outline of what you want to do, so I'll try to go down your questions and offer thoughts on what you already have to help you out in making more concrete decisions on how to organize your time.
--> A few days in Rome at the beginning sounds perfect, I would say 3 days is a good amount to also give you a chance to see most of the main sights and get over the jet-lag. You might also add in the last night out before your flight to spend it in Rome, depending on the time you have your flight to make it easier to get there on time.
Ok so it seems you're planning on 4 weeks overall in all of Tuscany and, yes, south to north makes sense but considering you make your way back to Rome to fly out, you can most definitely plan on making a "circular" route or at the very least, not overlapping.
I believe you should plan your itinerary based o when you'll have/require having a car and when you don't. A car is most definitely not needed in Florence nor in the main towns, but it is whenever you want to visit the smaller towns and villages.
Also, as far as Emilia Romagna, I've personally explored the bigger towns (which are all very well connected with train service) and not much of the countryside, just because I'm still exploring Tuscany
. So if you're not particularly interested in small towns in Emilia Romagna, I would suggest not planning to have a car at all for that part of the trip.
If you're planning on spending 2 weeks in southern Tuscany to explore the area from the start, you definitely NEED a car during this part. For that reason, I would recommend not staying in Siena and not heading directly there. So taking a train to Orvieto (or to Chiusi, as another option) makes perfect sense. Do you want to explore Umbria as well?
If you're thinking of exploring Chianti area and San Gimignano, it might make sense to include that while you have the car, so let me suggest this:
a week in southern Tuscany, then moving up for another week in the area between Florence or Siena and from here explore Chianti, Pisa, San Gimignano. Driving from there to the even Lucca is not very far, especially if you stay in the area north of San Gimignano. You can explore Siena while either you're south of Siena or north.
Then giving the car up, returning car in Pisa or Lucca and from here consider only public transportation. Take train to visit Cinque Terre, spending 2 nights there, then only then head back to Florence and then spend your week here. From Florence, head north to Bologna and any of the towns you wish to visit. Return via train south to Rome direct, to end your trip.
This way you have car while you need it, then depend on public transport and you have less overlapping - from Emilia Romagna you would have to do a wide circle to get to CT if you left it till later.
What do you think so far? I can offer more recommendations on places once you figure out if this order works for you! Let me know