I'm afraid i've got about the same questions as spumco and then some. I got the cables with the batteries installed today and followed your process, changed the config on each of the drives via the physical buttons and updated the relevant parts of the ini. I hadn't set up homing in any particular way before so i didn't have any of the stuff you commented in the hal file, though i was able to trigger homing and they would reference correctly against the inductive sensors even without any special config in the hal.
It'd seem like when i start linuxCNC the axis start on random positions. I get out of range errors if i try to home as is, and if i jog them into range and home after, i usually get amplifier faults. Am i misunderstanding what you mean by reference run? is there somewhere else in the drive's software where the homing needs to be triggered?
Besides that, my kinematics are the same as yours, with dual Y drives, and i'm wondering how gantry squaring works in this mode.
Edit: Ok, i think i sort of understand now, the config you have commented afterwards, you do need for the initial setup. However, where is request-cia-homing and start-cia-homing coming from?
github.com/rodw-au/cia402_homecomp
uses different names, not sure if what you're using is equivalent. I'm trying to get the initial config to get the homing done before turning off all the config now.