Unfortunately, the Stepconfig wizard predates the separation of Joints from Axis. Back then setting up a machine like this was not a trivial task. And it still isn't, but it has been greatly simplified. I'm not even sure if the Stepconfig wizard in Master even builds true JA compliant configs or if it just builds the old style config, then lets the auto convert script change it.
I think at this point the simplest option to building a config such as you are after, is to use Stepconfig to create an XYZA config, then modify it to be the XYZX config you need. Make the config, ignoring most of the settings for the A-axis (as you will be deleting or replacing most of them.) But do set up things like limit and home switches for the A.
Once you've built the config, copy and paist the settings for JOINT_0 to JOINT_3 in the ini file replacing what was there. Delete the section for AXIS_A and then make the nessisary changes to the KINS and TRAJ sections.
You might not even need to make any changes to the hal file, unless you want to change any arbitrarily named signals from referencing the A axis to something like X2.
