Today after hooking up the oscilloscope we were able to verify a few things and start getting values to count.
Wiring
We took a standard PWM cable and connected as follows:
Red wire to the 200 Ohm resistor and then to Pin #2 of the motor.
The White wire connects to the motor side of the resistor/Pin #2.
Then Black wire to Pin #4.
Plugged this into an Analog Channel on the RoboRio (5V power supply).
Code
We used a AnalogTrigger (Java) to tie into the analog signal and set its limits based off the values we were getting from the oscilloscope.
AnalogTrigger trigger = new AnalogTrigger(0);
trigger.setLimitsVoltage(3.5, 5.0);
boolean inWindow = trigger.getInWindow();
The next steps will be to keep track of this count and setup equations to be able to set the angle of the mechanism. Hope this is useful if other teams are looking to use these motors and its hall effect sensor.