The problem seems to be within the controller.
While the 5v appears on the input pins to the controller box, the output pins on the "parallel I/O" socket switch from 0.09v to 3.69v when the X or Z limit switches are operated, but the Y output stays at 0.9v.
I assume therefore that there must be an inverter/buffer stage between the switch input and the output socket, and this is where the problem lies.
Further investigation shows a 7414 type octal inverter, possibly wired up as four shmitt triggers(I think - it's been 50 years since I was doing this sort of thing !) for each of the four steppers, xyyz.
This feeds signals to a pair of 74LS244's and various and and nand gates, before the four L297 controller chips..