What version of stepconf are you using? the latest stepconf allows for loading three parports. The fist parport would be used for stepping axis the other two would need to be connected to signals in the custom HAL file.
so to re-cap you can :
load three parports with step conf
The first one stepconf helps you set up signals for.
the other two must be connected in a custom HAL file.
The custom HAL file will not be over written.
The INI and regular HAL file WILL be over written.
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