I don't think you're giving yourself enough time to get from JFK to the city and vice vera. Using the A train with a bus transfer is about 1 hour 15 minutes but with weekend service I would give myself 1 hour 30 minutes to be on the safe side. An alternate route is transfering to the Q10 bus from the E/F in Kew Gardens (forgot the exact name of the stop) but I am not sure how long that takes.
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