Thanks Matt,
I'm using a IRF 540 npn transistor to act as a switch. I've connected the emitter to the counter ground, and the base to the counter output. What this is supposed to do is apply the PWM coming from the DAQ to the switching transistor that is connected to a power supply. As far as the LabView part I used a shift register like you recommended and Boolean logic to compare the set value to the measured value which is wired into a case structure and either increases or decreases the duty cycle depending on the status of the difference in RPM. I've included the VI as an attachment.
-Joey
