I went back and edited the pncconf-generated INI file as follows:
-commented out these lines:
#HALFILE = custom.hal
#POSTGUI_HALFILE = postgui_call_list.hal
#SHUTDOWN = shutdown.hal
-changed [KINS] and [TRAJ] coordinates to XYZY (were XYYZ)
-put joint 3 as Y2 and joint 2 as Z
-made step scale value for Y2 negative
And edited the pncconf-generated HAL file as follows :
-changed stepgen.04.position-scale and stepgen.04.velocity-cmd values to fix charge pump frequency
-removed toolchange, coolant, probe, HALUI, and home / limit switch sections (tried commenting out each section one at a time so I could see the effect)
The PID stuff is apparently important - if you comment that out, LinuxCNC will start up fine, the charge pump works, and you can home the axes, but the second you go to jog, it faults. So that stuff should be left alone in the INI and HAL files. The "closed loop stepper signals" sections in the HAL file should be left alone too. Working INI and HAL files attached.
Once I was able to jog and issue MDI commands, there was only one thing left to check - the "spindle". Grabbed my laser safety googles (and respirator) and was able to turn it on and off via MDI. I loaded up an old nc file that I had for a wooden bracket and ran that on some scrap cardboard, which came out swimmingly. See attached pic.
Lesson of the day is don't delete stuff you're not really sure about and if you are going to delete stuff, trying commenting one thing or section out at a time.
Thanks again for your help, Peter!