Proximity limit switch problems

[JAZZCNC]

Mapping these back to the pins in the control box this leave S1 unallocated which doesn't seem right.

Ok Well first of all under stand that you have 4 spare Inputs labelled S1-S4 and can use any you like for anything you like. In this case you have assigned S2 for Limits and S3 for homes. Could easily be S1 limits and S2 home doesn't matter so long has you Set the correct Pins inside Mach3 inputs. ie: S1 = pin2 so set Limit's ++ and Limits-- to pin 2.

S1, S2 and S3 on my machine seem to relate to S1 - Y, S2 - X, S3 - X prime home. I've tried to match these up with Home 1, 2, 3 and Limit 1, 2 in the diagram. Hopefully you can offer some guidance if I've got the order wrong.

Now this is were it changes regards Homing because you have 2 switches Homing one Axis to square the gantry.
So now you need to have the Second Switch (Home2) on X using it's own Input. The other switch(home Prime) can still be wired in parallel with the Y and Z axis so share same Input.

Now you wire it just the same regards Brown and Blue but will need an extra wire for the (home 2) signal (black) which will go back to it's own input.

So now you will have connections on the control will go.

All Limits = S1
HOME X(prime) Y & Z = S2
HOME X(Home1) = S3

Would this setup eliminate the need for the mechanical e/stops I have or do I still need those on each axis? I would rather get rid of them if I could.

Not sure what your meaning here about Mechanical E-stop.?

E-stop should be a Button that gets pressed and SHOULDN'T be removed under any circumstances. It should also be wired and setup in such away that it doesn't just send signals to the control software, like your doing in this instance with limits.

The E-stop should remove power to any devices that are relavant Ie drives, Vfd, spindle etc and then inform the control software an E-stop has happened. Often this is done thru the use of relays with low voltage controlling high voltage devices but this is a whole new area which I won't get into now. Just search the forum to find out more.

BUT what I will say is DONT REMOVE THE E-STOP and DONT rely on SOFTWARE controlled E-STOP.!!