See http://electronics.stackexchange.com/questions/4951/how-do-i-calculate-how-fast-a-capacitor-will-discharge/18696#18696 for the relationship between capacitance, voltage, and discharge current, and how to calculate the discharge time.

How are you charging the capacitor? The 6.3V rating on your capacitor only indicates the maximum voltage that can be applied to it without being damaged.

What is the 39 ohm resistor you have? Please draw a schematic of your circuit. Also note that the motor will have an inrush current at startup that is many times higher than its rated current. This will affect the runtime considerably when the total stored power is so low.