When running the FOC IP in the IIO Scope the "Matlab Controller" option must be selected and the encoder must be plugged in. The regular controller runs only with the hall sensors.
What do you mean by "I wiggled the wires on the top of the motor and it started spinning"? Just by shaking the motor's leads or the encoder wires the motor started to spin?
Smoke is not too good, but it might be that your motor is still alive. Can you try to spin it with the regular controller?
Thanks,
Andrei