When does the bike die? Does it happen with freshly charged batteries or maybe after 10-12 miles when you have used up half the range? Does it stay dead or does it recover for a little more riding? If it recovers, can you feather the throttle and go on for a while? Do you have any voltage indicators on that bike? What I am trying to do here is make sure it's not a voltage sag problem from weak batteries as opposed to a real throttle failure problem.
Your motor kit has no pedal assist, right? It's all throttle. Do you know your cruising speed?
I have some experience with those same batteries. I run them separately on a little 36V motor. Put two in parallel for my 500W motor. They're about 4AH each when pulling 200 watts. I've seen them put put 20A peak per pack, but that will probably kill them. When I run them in parallel, I recharge in parallel too.
The cells in the packs are not crap, but they aren't really strong. I took two apart and made a 13S-2P (48V) battery with a good BMS, and found that when it got down to 46 volts, it would shut off from voltage sag. End of that experiment. It was 75 degrees that day too, How cold is it in NYC this week? 45F? That will kill range too.
I'm thinking battery because two controllers and two throttles did the same thing. I do agree that 2.4V is low. Should be over 4 volts. You're getting 4.3 volts on the supply wire?