pncconf does not change the firmware in the FPGA card, only mesaflash can do that
If you get a command not found error with mesaflash it probably means your LinuxCNC installation is not up to date
since mesaflash is installed on the latest linuxcnc versions
So for various reasons I would first update to the latest released version of linuxcnc (2.6.8)
and then use mesaflash to write the desired firmware to the 5I25 card
The hm2_5i25.0.pwmgen.pwm_frequency not found error is expected if the currently loaded firmware does not have a pwm generator
The readme pinout is not a real reference to the pinout, only
sudo mesaflash --device 5i25 --readhmid is
As the header in the printout says, the pinout table fields are:
Pin# (DB25 pin number)
I/O (GPIO number)
Pri function (always I/O port for HostMot2)
Sec Function (StepGen PWMGen etc)
Channel
Pin function (if not GPIO)
Pin direction (if not GPIO)