All of the counter setup should be outside the loop; only the DAQmx Write should be inside the loop. Have you looked at whether your code generates any errors? You can only set the duty cycle when the code starts because after the first loop iteration, your current code returns an error when you try to create the the DAQ task since the counter resource is already in use (by the task that was created on the first loop cycle). If you create the task only once, outside the loop, you won't have this problem.
Change the duty cycle by using the Duty Cycle input to DAQmx Write.
Why do you have a completely unused DAQ task being created outside the loop, and then cleared inside it? Also, clean up your wires - there's no need for wires to run underneath the while loop.
When you connected the PID output to the duty cycle input, did you probe the output from the PID to see if it's responding? The Duty Cycle input is 0-1 (for 0-100%). You appear to have the PID output range set to 0-5, why? The PID output range should match the limits of the duty cycle. Have you tuned the PID at all? You are unlikely to get any sort of good response from your system prior to tuning, and there are many resources available (the PID toolkit manual, other posts on this forum, and elsewhere on the web) to help you tune a PID loop.
