New build with recycled parts on a ridiculous budget 120cm*60cm work area

[Clive S]

I think the limit switches one wire to each input and the other wire to the shared gnd? I need 2 limit switches for my Y and 1 for my X can I reconfigure the Z axis limit to be my 2nd Y? I want to set linuxcnc up so it squares the gantry. I'm going to use microswitches for now but I might use inductive sensor instead do I simply find 12v for the sensor elsewhere and wire 1 wire to the Axis input and 1 to the GND?

You are going to have a problem with this bob because you won't have enough inputs to do what you are trying to do.
for instance that bob and most simple bobs only have 5 inputs. You will need two for the homing for the slaved axis. Then you have all the limits they can be wired in series to one input that leaves two. you have to home Z and the other axis. So the probe is out of the question.

Emergency stop run my stop button to it AND the outputs from the AM882 for stall protection.

The E/S button would not be connected to the stall on the EM882 This should be cutting power to the drives power supplies etc. though a contactor or whatever.

the 12-24v is that an input for driving the board? If not what is it used for. I thought the board was powered by 5v from the USB socket.

The 12-24v power is for the inputs and the 5V is to power the BOB. connect the two power -ve together. I would not use power from the usb for anything.

If you are using linuxcnc I would download the 2.8 master branch and get to see how it works. Also I would connect one thing up at a time and see if it works as intended then move on to the next problem.

edit:

What does the relay jumper do?

this changes what pin 17 will do, you have two choices either the relay OR the B axis dir. You can't have both.