Your 9V battery was not full, that is why your motors are still alive.
If you regulate the voltage at 3.6V then the motor will draw the current it needs to work.
If you know the running current of the motor you can calculate the value of the needed resistor as to drop 5.4V across it and leave the other 3.6V across the motor. I said running current because the starting current of the motor is larger than the current after the motor has started. This will limit the starting torque of course. If you want to keep in some way the starting torque put a 3300uF capacitor in parallel with the resistor.
If you regulate the voltage at 3.6V then the motor will draw the current it needs to work.
If you know the running current of the motor you can calculate the value of the needed resistor as to drop 5.4V across it and leave the other 3.6V across the motor. I said running current because the starting current of the motor is larger than the current after the motor has started. This will limit the starting torque of course. If you want to keep in some way the starting torque put a 3300uF capacitor in parallel with the resistor.