Reassembling the mill provided an opportunity to move the Y axis Home switch from the rear of the axis to the front. The key discovery happened during the teardown: I can get the saddle off the Y axis dovetail by removing the gib, without sliding it off the front, which means a front switch can remain firmly glued in place.
A few random hunks of steel and a wire nut held the switch in position while the epoxy cured:

The switch actuator bottoms out with the saddle just touching the preload nut, so the saddle can’t dislodge the switch: the switch trips just before the saddle hits the nut, at which point all motion stops and the motor stalls.
Moving the switch means I can remove all the gimcrackery that poked the rear switch with the tooling plate in place; I was never happy with that setup. I also removed the small block that trapped the rear end of the Y leadscrew, under the assumption that, as I haven’t yet dropped anything on the leadscrew, I probably won’t. That adds about 1/4 inch to the maximum travel and allows the tooling plate to whack into the column.
The switch wire runs along the stepper cable, a tidy technique that hasn’t introduced any glitches into the shared Home signal from the X axis drivers:

The Y axis now seeks the Home switch in the positive Y direction, so that stanza in Sherline.ini
looks like this:
[AXIS_1] TYPE = LINEAR MAX_VELOCITY = 0.400 MAX_ACCELERATION = 5.0 STEPGEN_MAXACCEL = 10.0 SCALE = 16000.0 FERROR = 0.05 MIN_FERROR = 0.01 MIN_LIMIT = -0.5 MAX_LIMIT = 4.90 BACKLASH = 0.003 HOME_IS_SHARED = 1 HOME_SEQUENCE = 2 HOME_SEARCH_VEL = 0.3 HOME_LATCH_VEL = 0.016 HOME_FINAL_VEL = -0.4 HOME_OFFSET = 5.125 HOME = 5.0