Since the PMON (for pulse measurement) and HSCDEF (high speed counter) share the same input pins, it means that they are mutually exclusive. i.e. if a pin is defind for PMON it cannot be used for HSCDEF. The last defined function prevail.
What you can do is to use input 3,4 as PMON to get two channels of pulse width measurement, then connect a wire from pin 3 to pin 5 and use HSCDEF channel #2 for high speed counter measurement.