The reason it is only happening when using the IB4200s is because of the cells. IB4200s have a higher voltage than other cells, which is why even though they are the least reliable cells you can get all the top touring car racers won't use anything else. It sounds like using the 3700s the motor is just within its limits and using the 4200s just goes over the limits.
A 19 tooth pinion is too big for 12 turn motor, the 16 tooth pinion should help but the motor should not be getting too hot to melt solder. As the motor has recently been rebuilt if the timing on the endbell was not set correctly and is too far advanced the motor will overheat very quickly. Lowering the timing on the endbell will reduce the current draw so making the motor run cooler.
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