Welcome to FT. As many of us replying are experienced fliers there is not going to be any really positive help.
I have flown many times in and out of JFK on international flights and know from that experience to leave plenty of time to the point of booking the later of two flights, in this case the 7:25 in stead of the 5:45 so to give an extra 80 minutes. Doing so means that the incoming flight will be early, immigrations and customs will a breeze, no long walk to another terminal, and TSA will have short lines. In other words I could have made the earlier flight, instead I head to the lounge for a beer. Had I booked the earlier flight the complete opposite would have happened. Not quite the OP's case but close.
Sidebar: about the only US airports that I will book an 85 minute layover with an international flight are Atlanta and Detroit. I know those airport well, have Global Entry, and am able bodied.
As for the issue of not getting through TSA in an reasonable manner. Therein lies the real issue. One needs to be persistent. I have gotten plenty of pat downs as I refuse the scope. Sometimes getting a TSO can be a long somewhat punitive wait. A 35 minutes wait is ridiculous and is really the only airport related complaint.
What I really do not understand is why your traveling companion did not wait for you. Not going to say more about that.
Leaving most everything with your travel companion so they could go ahead reminds me of one of my early international travel stories. A friend and I were taking an evening train in Europe. While waiting on the train I discovered something was missing from my duffle that had been in a bag locker at the train station. The train was scheduled to leave in 10 minutes. So I left everything with my friend on the train and ran back to the locker. As I did that I thought, if the train leaves I could be a world of hurts as I do have my passport or any money. Nothing was at the locker so I ran back to the platform only to see the train doors closing and the train begin to move. My friend had opened the window and was saying something to me when I said get out of the way, made a running leap, and dove through the window which caused quite the commotion in the car. Then the train stopped. We figured the controller saw my performance and was coming to boot us from the train. It never happened. The train was just adjusting its position at the station. It pulled out on time a few minutes later. Fortunately I can look back and laugh at my naivety (others can too, so feel free to do so).