configuring a rotary axis on a CNC Rrouter

On the 3 axis ini file:
The joint 3 section must be under the joint 1 section of AXIS X.
The hal file for that ini is set up as XYZA, not XYZX as you have it set in the ini.
As you have it set, you have a 4 axis setup that has outputs active for the first 3 axis.

On the 4 axis HAL file:
remove all lines with "setp parport.0.pin-02-out-reset 1", you are reseting the parallel port so you do not need to reset pins, and the pin 4 is written in two lines
on the 4 axis ini file, again the joint 3 is in the wrong place, it has to be at the Axis X section, under joint 0

The joints that are for the same axis, the X axis in your case must have "HOME_SEQUENCE = -1" for both joints.
Editing hal and ini files is easy, just open them with a text editor and edit as described, save and try to start Linucnc again to test the changes.

Copy and paste error:
You reset pin 04 twice, and pin 16 never.

It might not be that, though.

In principle LinuxCNC can only step at half the base thred frequency, turning a pin on during one thread cycle, then turning it off on the next.

The parallel port driver has an extra function called "reset". If a channel is specified with reset active, then the driver sets it high when required on one thread cycle, then, in the same cycle, but at the end, it checks to see if the "reset time" has elapsed and resets the registered pins back to zero. If the time has not elapsed it waits until it has and then resets (note that this wait is blocking, and should not be too long)

linuxcnc.org/docs/2.7/html/hal/parallel-...ml#_using_doublestep

Setting STEP_SPACE to 0 in the HAL / INI is the hint to the driver that you want to use reset. If you set the step space to zero )as you did) but don't add it to the reset list, then the write thread will only ever set the pin high, and with no reset function to set it low, you will get no steps.