[aeastet]

Your set point should be 1000 as long as the input to the PID is in RPM and the process values is in RPM. If the input to the system is pulses then you are going to read pulses on the process variable and change the motor output.

You have two options here:

One: figure out how many pules it takes to get to 1000RPM and have that be your input. I your case 120 (counts in one revolution) * 1000 RPM = 120,000 pluses. This way you could read pulses into your PID and it would adjust. In this case 120,000 would be your input to the setpoint.

Two: convert pulses to RPM and feed this into your PID loop. I this case you you have the set point of 1000 and you would read RPM.

Either way will work.