5 nights = 4 full days + a partial day on the day of arrival
- 1 full day will be needed for Siena
- 1 full day will be needed for Florence (assuming you take one day trip only to Florence)
- 1 full day I would devote to Pisa only, primarily because from Siena it will take 1h50min to drive there (via Poggibonsi-Castelfiorentino-Empoli). On the way back, if you have time, you could visit Certaldo (Giovanni Boccaccio's birthplace), which is along the way.
- 1 full day I would devote to San Gimignano (about 45 min from Siena), plus something closer than Pisa, which you should have visited separately (see above). I would consider visiting something else close to San Gimignano, like Monteriggioni (which is sort of on the way from Siena to San Gimignano, about half way) and maybe even Colle Val D'Elsa (also next to Monteriggioni). Volterra could be another choice that you could pair with San Gimignano. So you could do a loop Siena to San Gimignano (50 min), then San Gimignano to Volterra (50 min), and finally return to Siena from Volterra (1 hour).
In Florence I would park at Porta Romana (see link below)
https://maps.app.goo.gl/27aJovt5YugWEh4NA
From the lot you can walk to the sights and you would need to pass through Ponte Vecchio.
Follow the navigator and pay attention to the bus lane going there (you must turn right on Via del Gelsomino).
In Pisa I would park here:
https://maps.app.goo.gl/F7PetCLctyUdJ5pX7
5 min walk to the Piazza Duomo (leaning tower)
If you have a chance to rent a car before Orvieto, I would consider driving from Orvieto to Siena. The train takes forever while if you drive, from Orvieto to Siena it will take you only 1h30min
You might consider returning the car in Florence instead, and take the train from Florence. Too many changes from Siena. you could also drive all the way from Siena to Como, but it's up to you. The advantage of a car is that you don't need to worry about hauling luggage on and off trains. The disadvantage is that the drive will be long and boring (especially for the person doing the driving), albeit it is all freeway.