I have figured out how to measure timing. Now it is a matter of writing the code for it. The back emf of the motor is not dependent on timing, whereas the hall sensors obviously are. So to measure timing you need the delta between the rising edge of the sensor pulse and the rising edge of the back emf. Here are a couple of scope pics that I did. The first one the can timing on the motor is set to 0*, you can see that the rising edge of the back emf and the sensor line up. The second pic has timing advance of about 40*, you can see that the back emf lags behind the sensor.