Thank you all so much, I'll start with that and report back later.

Thanks a lot for your reply, i'm very familiar with all kind of hardware, but codes, commands and macros are realy not my strenght. By enable Z to go below zero I mean that I have a macro for zeroing all axis at a current pozition and switch to work coordinates and the foot switch macro will run after I zerowed xyz and this 2 mm will be -2, below zero, into my stock as you said. I would appreasiate some sample code, realy don't know where to start. Lets say I connect the switch to my x endstop, what shall the code be looking like?

I have an unusual task to complete. I want to trigger a macro with a foot switch. I have a small CNC machine for PCB milling and drilling controlled by Duet WIFI, which is working fine, but I want to make a simple mod to drill single holes in PCB with both hands free. The macro should enable Z axis to go below 0, set moving speed and move Z 2mm down and back and should be triggered by foot switch. How do I connect the switch and what the code should be for the macro? Any help will be highly appreciated. I'm running firmware 2.05 on a Duet WIFI.

Thank you, problem solved, but it was really unexpected.....

Hi, I have an issue after I upgraded my Duet 3 this morning. I'm using the Duet 3 board with R-pi combo in CNC mode and I used " sudo apt update "
" sudo apt upgrade " connected to the Rpi with Putty. The upgrade went fine with no errors. After the upgrade the Z-Probe in the Duet Web Control 3.1.1 reads 1000 when not triggered and 0 when triggered. My Z probe is just a simple CNC probe which triggers when the tool touches the aluminum block. For endstops I'm using motor stall for homing and it works perfectly. The probe is connected to IO3 on the Duet 3 board. It was working perfectly until yesterday before the firmware upgrade. Below is my endstops and probe settings from the config.g file:
; Endstops
M574 X2 Y2 S3 ; configure sensorless endstop for high end on X and Y
M574 Z2 S3 ; configure sensorless endstop for high end on Z

; Z-Probe
M558 P5 I1 C"io3.in" H2 F300 T2000 ; set Z probe type to switch and the dive height + speeds I1
G31 P500 X0 Y0 Z0 ; set Z probe trigger value, offset and trigger height
M557 X5:500 Y5:500 S50 ; define mesh grid

Changing the invert parameter I1 to I0 and back doesn't work anymore and it's not recognized from the firmware - see below the console output when sending M558 with both parameters:

5/23/2020, 10:57:24 AM M558 I1
Z Probe 0: type 5, input pin io3.in, output pin nil, dive height 2.0mm, probe speed 300mm/min, travel speed 2000mm/min, recovery time 0.00 sec, heaters normal, max taps 1, max diff 0.03

5/23/2020, 10:58:43 AM M558 I0
Z Probe 0: type 5, input pin io3.in, output pin nil, dive height 2.0mm, probe speed 300mm/min, travel speed 2000mm/min, recovery time 0.00 sec, heaters normal, max taps 1, max diff 0.03

and the console output after changing the parameter I0 I1 in the config file and sending M119:

with I1:
M119
Endstops - X: not stopped, Y: not stopped, Z: not stopped, Z probe: at min stop

with I0:
5/23/2020, 11:02:15 AM M119
Endstops - X: not stopped, Y: not stopped, Z: not stopped, Z probe: at min stop

I did change the parameter maybe 30 times, restarting the board and the whole system every time with no luck. I believe this is a firmware problem because it happened after the upgrade I did this morning. Please advice how to solve this weird issue.

@droftarts I cannot express how much I appreciate your input on this, just to confirm, I need to make this marked in red two sections of the belts from the joiner to the gantry mount parallel , correct, see the photo below:

@dc42 Thanks for your help, you were 100% right to say "follow the instructions". All movement and homing works perfect now (in terms of direction)

@droftarts Thank you! I finally managed to sort out the motor movement, as dc42 said more than ones, "follow the instructions". All moves and homes properly now.

Regarding your note on the belt connections to the X carriage, yes, I used the design from the SecKit SK-Go and was wondering why the XY joiner pulleys are not combined, and now thanks to you I know. I will complete all the wiring and see how it prints and when i see that its not printing properly, I'll change my design accordingly, thanks for the heads up, I really appreciate it!

@droftarts Thanks for the input. My machine configuration is exactly the same as on the photo, with two differences, my X and Y motors are mounted at the back side and I'm using Y high and X high endstops, so the gantry homes at the right back side of the printer at X340 Y340, Origin at X0 Y0 at front left corner. I tried swapping the two motors and went bad, everything moves in different direction. Photo below:

@dc42 I did follow the instructions and everything went easy and well, except that Y is X and X is Y ( when I try to navigate from the Machine Movement). If I send G91 followed by G1 S2 X10 F3000 as per the instructions the gantry goes towards + X +Y , same for G1 S2 Y10 F3000, it moves in +X and -Y. Z moves properly, X and Y homing is OK, the BL touch is homing Z correctly, Z offset is fine, If I could swap the X and Y in the Machine Movement section on the web interface I wouldn't have a question (and I still don't know if I really have a problem). Ill post my config.g (drives and endstops section) and homeall.g belo9w:

; Drives
M667 S1 ; switch to CoreXY mode; M669 K1
M569 P0 S0 ; physical drive 0 goes backwards
M569 P1 S1 ; physical drive 1 goes backwards
M569 P2 S1 ; physical drive 2 goes forwards
M569 P3 S1 ; physical drive 3 goes backwards
M584 X0 Y1 Z2:4 E3 ; set drive mapping k
M350 X32 Y32 Z32 E32 I1 ; configure microstepping with interpolation
M92 X160.00 Y160.00 Z3200.00 E818.00 ; set steps per mm
M566 X1000.00 Y1000.00 Z24.00 E300.00 ; set maximum instantaneous speed changes (mm/min) (Z was 24)
M203 X8000.00 Y8000.00 Z400.00 E8000.00 ; set maximum speeds (mm/min) (Z was 180)
M201 X500.00 Y500.00 Z120.00 E3000.00 ; set accelerations (mm/s^2) (Z was 100)
M906 X800 Y800 Z800 E900 I40 ; set motor currents (mA) and motor idle factor in per cent
M84 S30 ; Set idle timeout

; Axis Limits
M208 X0 Y0 Z0 S1 ; set axis minima
M208 X340 Y345 Z700 S0 ; set axis maxima

G91 ; relative positioning
G1 H2 Z5 F6000 ; lift Z relative to current position
G1 H1 X320 Y320 F3000 ; home X and Y
G1 H1 X320 ; coarse home X
G1 H1 Y320 ; coarse home Y

G90 ; absolute positioning
G1 X175 Y175 F6000 ; go to MidBed and home Z

G30 ; home Z by probing the bed
G29 S1 ; load heiht map automatically