Novamill - Mach3

[m_c]

I can probably guess why homing and limits don't work then.

Denford for a while used inductive NAMUR sensors for homing, which are a sensor type designed for volatile atmospheres (basically a two wire sensor that changes resistance/current flow, so any wiring faults don't result in sparks). These are not easy to interface, but the original controllers used them, so I'm guessing whoever done the retrofit probably never changed them.
Instead they've probably modified the limit switch wiring to use them as home switches, as the limit switches would have originally broken the E-Stop circuit, but then they've never really implemented them. Or possibly disabled them because the Z has gone faulty.

Before you dismantle anything major, if the machine still has the big Harting multi-connector for connecting the machine to the control box, unplug that and very carefully look to make sure all the pins and sockets are in position and the same height. I've seen them become unseated, so they don't make contact.

[Deck36]

The homing situation makes a lot of sense now, from what you've said. Can the physical switches be used for homing or is that impractical?