I think your allocation is great, except for maybe, and this is only my own preference for smaller places over large cities, I would borrow one night (or even 2 nights if it were me) from Rome and give at least 4, and maybe 5 nights to Cortona.
It's not that Cortona itself needs 5 nights (less than a day is enough for Cortona), but with a rental car, from Cortona as a base, you can visit a lot of places within one hour or so drive. To name some of the closest to Cortona (in alphabetical order):
Anghiari, Arezzo, Assisi, Bagno Vignoni, Buonconvento, Castiglion del Lago, Castiglion Fiorentino, Cetona, Chiusi, Chianciano Terme, Civitella, Cortona, Gubbio, Loro Ciuffenna, Lucignano, Montepulciano, Montalcino, Perugia, Pienza, Poppi, San Quirico d'Orcia, Sarteano, Siena, Spello.
They are all beautiful and quaint, but of course you don't have weeks to visit all of the above, so I bold faced the most famous.
You can rent a car using a consolidator such www.autoeurope.com or www.kemwel.com (they are actually the same company after a merger years ago). Most of us in this forum use the above. They work primarily with Avis, Budget, Europcar, Hertz, which are the major companies in Italy.
You would pick up the car in Florence at the end of your visit just before heading out of town (any pick up location will do, but picking up at the airport carries additional charges). There is no risk of getting a fine in the ZTL on your way out. That risk exists only on re-entry, if you return the car to Florence (which is not your plan anyway).
You can return the car in Rome or, if you happen to choose Hertz from the above consolidator, you could even visit Orvieto on the way to Rome and drop off the car at Orvieto (only Hertz has a facility there).
Rome has many locations throughout the city. Which one to choose will depend on which rental company you select. We can help you there once you make that selection.
Cortona has a ZTL where traffic is restricted, therefore with a car choose lodging outside the ancient city center or at least that is accessible by cars (preferably with parking on the premises). There are plenty of countryside hotels and villas all around Cortona.