Traveling to Florence from JFK with a layover in rome, i have a few questions

If your flight connection is all booked on one ticket, then your checked baggage will be checked all the way through, and the airline will take responsibility for getting you all the way to Florence; therefore that connection time is fine. You will go through passport control, which often has a line; if the line is long, look for anyone helping people who have immediate departures.

If you second flight is booked as a separate ticket on an "independent" budget airline with no interline agreement, then you will have to collect luggage and don't have much protection in case of flight delays.

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• 1h30m is enough if your inbound flight is on time.
• Yes, you have to go through Passport Control (immigration) first when you arrive at T3, then through security again at the T1 (Domestic). If you have checked baggage, it will go through all the way to FLR (you don't have to retrieve it and go through customs in Rome. Customs is in Florence).

Your flight from FCO to FLR is on Alitalia. As mentioned by Laura above, if it's one ticket, the airline will re-book you on the next flight if you inbound flight is delayed and you miss the connection.
The only problem is that there are only 3 flights to FLR: one in the morning (at about 10am), one in the afternoon (after 3pm) and the last one at night (after 9:30pm).
Therefore if you miss it and the next flight is 6 hours later, it's faster to go by train. There is a train every 20 min. to Florence from Rome, and it takes 90 min. from Roma Termini (Roma T. is only 32 min. by train from the airport).

That is why I will not buy an Alitalia/Delta airplane ticket to Florence with layover in Rome. Once you land in Rome, the train is a much better option, since there are so few flights to FLR.

I made that mistake once. My flight from FCO to FLR was diverted to Pisa at the time as FLR was temporarily closed. To add insult to injury when I landed in Pisa there was a rail workers' strike affecting ONLY the Railway workers in Tuscany (therefore the trains from Rome to Florence were running, but not the trains from Pisa to Florence). I had to take the bus instead and I made it to my parents' home in Florence at almost 4pm. Since my flight from JFK landed in Rome before 7am, had I taken the train directly from Rome to Florence I would have been home before 11 am. I hope you are luckier than I was that time.