LinuxCNC + Mesa 7i92TF + Gecko G540. Docs are useless. Help, Please!

You can setup gantry machines with pncconf:

 

Thank you.

This essentially gives me the HAL I created by hand. This does not bind the two Y axis motors together. Launching LinuxCNC with this HAL still shows me the 4 joints, until I home the Y axis where it sits, which is not where I need it to be homed.

I pored over the HAL and INI files created by PnCConf using your settings multiple times, and cannot see what I am doing wrong. There seems to be no difference between what it generated by selecting Y2 Tandem StepGen, and my manual HAL where I simply copied the Y axis settings, pasted them in, and changed every instance of Y to Y2, and 01 to 02.

See the right side of PCW's screenshot, did you choose the pin/home/limit switch for Y2 axis?
More importantly, does the machine have a separate switch for each joint of the Y axis?

The machine does not currently have limit switches. I have the limit switches commented out.

I recently rebuilt the machine from the ground up. As the software is an upgrade, I am trying to get it working in its most basic form before adding limit switches, a touch plate, a probe, and a tool changer.

Do I have to have hardware limit switches set up in order to get the gantry to work correctly?

Apologies if that is a dumb question. I have found the documentation incredibly lacking, which is why I’m here on this forum.

Yes, you do need switches for each joint for tandem axis to work properly and be able to square the gantry anytime the machine homes.
If you do not have switches, you can just wire both Y drives to the same output on Mesa and make a new simple XYZ config.
BTW, you can make as many configs as you like, test, experiment, try things out, have a blast...
And feel free to ask as much as you like, you are always welcomed.

Actually when you know where to look, the documentation runs to hundreds of not thousands  of pages.
setting up a gantry machine requires joint axes and is covered in the  homing docs.  linuxcnc.org/docs/stable/html/config/ini-homing.html
You usually need to read that link about 10 times before it makes sense.
Briefly you need a home switch on each joint (eg a joint is a motor). When set up right with negative  home_sequence, the first side of the gantry stops and waits for the other side to catch up before moving in unison. Gantry Squareness is adjusted by setting the home_offset in the ini file