I'm starting to build a CoreXY printer (this one), but this design has 6 limit switches (Min & Max in each plane) and the Duet board only has plugs for 3.

Is it possible to connect 6 end stops to the Duet board, or do I have to go with convention and use 3? I know that I should only need 3 (one of which will be an IR Z probe), but I have a tendency to be over-cautious! It's just the thought of X or Y going flat-out into the side without a switch that concerns me...

RepRapFirmware (like most firmwares) uses the switches for homing only. While it would be possible to wire 3 additional switches to a Duet, you would need to modify the firmware if you wanted the switches to be active all the time. IMO it isn't necessary, because once you have homed the printer, the firmware will prevent it from moving outside limits.

However, I intend to add a facility to attach a pause button in the near future, and possibly also an emergency stop button. You could wire 3 extra switches in series and connect them to the emergency stop input.

But my advice is not to bother with extra switches, just set up the config file correctly, and use rubber pads or similar as mechanical endstops.

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Large delta printer [miscsolutions.wordpress.com], E3D tool changer, Robotdigg SCARA printer, Crane Quad and Ormerod

Disclosure: I design Duet electronics and work on RepRapFirmware, [duet3d.com].

I like the idea of an emergency stop button, something that's lacking on my Prusa i3 with RAMPS. With that printer I have to look at the screen, locate the emergency stop button in Repetier Host and click on it. If I'm printing off the SD card then I can't even do that.