All working as expected now thankyou.

I think the key change was setting the correct Z height

M208 X305 Y332 Z350 S0 ; 

now;

M208 X305 Y332 Z950 S0 ; 

Full Gcode;

950 ; Configuration file for Duet WiFi (firmware version 3)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool v3.1.4 on Sat Sep 05 2020 23:57:30 GMT+0100 (British Summer Time)

; General preferences
M80					       	; Turns on the ATX power supply
G90                                            	; send absolute coordinates...
M83                                            	; ...but relative extruder moves
M550 P"BLV MGN Cube"                           	; set printer name
M669 K1                                        	; select CoreXY mode

; Network
M552 S1                                        	; enable network
M586 P0 S1                                     	; enable HTTP
M586 P1 S0                                     	; disable FTP
M586 P2 S0                                     	; disable Telnet

; Drives
M569 P0 S0                                     	; physical drive 0 goes backwards
M569 P1 S1                                     	; physical drive 1 goes forwards
M569 P2 S1                                     	; physical drive 2 goes forwards
M569 P3 S0                                     	; physical drive 3 goes backwards
M584 X0 Y1 Z2 E3                               	; set drive mapping
M350 X16 Y16 Z16 E16 I1                        	; configure microstepping with interpolation
M92 X200.00 Y200.00 Z800.00 E415.5             	; set steps per mm
M566 X600.00 Y600.00 Z24.00 E300.00            	; set maximum instantaneous speed changes (mm/min)
M203 X20000.00 Y20000.00 Z600.00 E2000.00      	; set maximum speeds (mm/min)
M201 X3000.00 Y3000.00 Z100.00 E5000.00        	; set accelerations (mm/s^2)
M906 X1500 Y1500 Z1500 E1100 I30               	; set motor currents (mA) and motor idle factor in per cent
M84 S30                                        	; Set idle timeout

; Pressure advance
; M572 D0 S0.05	

; Axis Limits
M208 X-23 Y0 Z0 S1                            	; set axis minima
M208 X305 Y332 Z950 S0                        	; set axis maxima

; Endstops
M564 H0					       	; allow jog without homing
M574 X1 S1 P"xstop"                            	;
M574 Y2 S1 P"ystop"                            	;
M574 Z1 S1 P"zstop"                            	; configure Z-probe endstop for low end on Z

; Z-Probe
M558 P1 H5 C"^zprobe.in" H5 F250 T9000 R0.5	; set Z probe type to switch and the dive height + speeds
G31 P500 X-2 Y-16.4 Z1.40                      	; set Z probe trigger value, offset and trigger height
M557 X10:292 Y5:300 P5                       	; define mesh grid

; Heaters
M308 S0 P"bedtemp" Y"thermistor"T100000 B3950 C0 R4700 A"Bed Temp"  	; configure sensor 0 as thermistor on pin bedtemp
M950 H0 C"bedheat" T0                          				; create bed heater output on bedheat and map it to sensor 0
M140 H0                                        				; map heated bed to heater 0
M143 H0 S100                                   				; set temperature limit for heater 0 to 100C
M307 H0 A466.3 C1262.5 D12.8 S1.00 V24.0 B0    				; Set PID for heated bed values
M308 S1 P"e0temp" Y"thermistor" T100000 B3950 C0 R4700 A"Hotend Temp"   ; configure sensor 1 as thermistor on pin e0temp
M950 H1 C"e0heat" T1                           				; create nozzle heater output on e0heat and map it to sensor 1
M143 H1 S260                              				; set temperature limit for heater 1
M307 H1 A340.0 C140.0 D5.5 S1.00 V24.0 B0     				; Set PID for hotend values

; Fans
M950 F0 C"fan0" Q500                           	; create fan 0 on pin fan0 and set its frequency
M106 P0 S0 H-1                                 	; set fan 0 value. Thermostatic control is turned off
M950 F1 C"fan1" Q500                           	; create fan 1 on pin fan1 and set its frequency
M106 P1 S1 H1 T45                              	; set fan 1 value. Thermostatic control is turned on

; Tools
M563 P0 D0 H1 F0                               	; define tool 0
G10 P0 X0 Y0 Z0                                	; set tool 0 axis offsets
G10 P0 R0 S0                                   	; set initial tool 0 active and standby temperatures to 0C

@nick9one1

figured it out - some weirdness with FTP. When I copy the www files to the SD manually it works.

@Phaedrux said in problems with pressure advance calibration:

retract on layer change

Thank you. Yes I have retract on layer change enabled

I've changed the z values you suggested and set the slicer to start the pressure advance at 0.035 in increments to 0.055. Printing now

I'm struggling to reconcile some of the instructions for wiring the ADAFRUIT LIS3DH to the Duet wifi 2 (some of the pin names on the accelerometer wiki dont exactly match what is silkscreened on the LIS3DH)
https://duet3d.dozuki.com/Wiki/Accelerometers

specifically;
(from the wiki)

MOSI (also called SDI) - There is no pin labelled this, maybe SDA?
SCLK - There is no pin labelled this, is SCL the same?

@phaedrux

I think I've found the problem. The second tool I added to config.g had D1 instead of D0.
The printer only has one hotend and extruder so they are 'virtual' tools that let me change filament print settings (temp, retraction etc.) in the slicer.

; Tools
M563 P0 D0 H1 F0   					 			 ; define tool 0
G10 P0 X0 Y0 Z0 								 ; set tool 0 axis offsets
G10 P0 R0 S0 									 ; set initial tool 0 active and standby temperatures to 0C
;
M563 P1 D1 H1 F0 						  		 ; define tool 1
G10 P1 X0 Y0 Z0 								 ; set tool 1 axis offsets
G10 P1 R0 S0 									 ; set initial tool 1 active and standby temperatures to 0C

@phaedrux

update - after making a few changes the hotend is now heating without the error.

The all metal throat is secured by two grub screws to the body/heatsink. Although properly secured, I think the throat was heating up, expanding slightly and making better contact with the heatsink, causing it to dump heat a bit quicker and triggering the error.
I've added some thermal compound to the throat/heatsink, re-tuned and can now heat from cold without any issues.

@dc42
thanks. I've tried a coupe of different cards with the same result.

The card I'm using is 100MB/s UHS class 1.

I've dropped the sample rate down to 100, and only for the X axis so the gcode looks like this;

G1 X-50 G4 S2 M956 X P0 S100 A0 G4 P10 G1 X50 F20000

the csv contains;
could it still be a wiring issue?

this is how its currently wired

Thanks. Yes I did that already. the Error: Board 121 does not have heater 1 was cleared by a restart. All working now, thanks!

it was alignment of the Y rails causing the problem. Unless they are perfectly aligned they can bind.

figured out the last bit. I didnt need to define a pin in M574 Z

M574 Z1 S2 

not

M574 Z1 S1 P"121.io0.in"   

full config.g in case it helps someone else.

; Configuration file for Duet 3 Mini 5+ (firmware version 3)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool v3.2.3 on Thu Jul 01 2021 17:21:30 GMT+0100 (British Summer Time)

; General preferences
G90                                              ; send absolute coordinates...
M83                                              ; ...but relative extruder moves
M550 P"BLV MGN Cube"                             ; set printer name
M669 K1                                          ; select CoreXY mode

; Network
M552 S1                                          ; enable network
M586 P0 S1                                       ; enable HTTP 
M586 P1 S1                                       ; enable FTP
M586 P2 S0                                       ; disable Telnet

; Drives
M569 P0.0 S0                                     ; X motor runs forwards
M569 P0.1 S1                                     ; Y motor runs forwards
M569 P0.2 S1                                     ; physical drive 0.2 goes backwards
M569 P0.3 S1                                     ; physical drive 0.2 goes backwards
M569 P0.4 S1                                     ; physical drive 0.2 goes backwards
M569 P121.0 S0                                   ; physical drive 121.0 goes backwards
M584 X0.0 Y0.1 Z0.2:0.3:0.4 E121.0               ; set drive mapping
M350 X16 Y16 Z16 E16 I1                          ; configure microstepping with interpolation
M92 X200.00 Y200.00 Z3200.00 E1000.00            ; set steps per mm
M566 X900.00 Y900.00 Z60.00 E120.00              ; set maximum instantaneous speed changes (mm/min)
M203 X6000.00 Y6000.00 Z180.00 E1200.00          ; set maximum speeds (mm/min)
M201 X500.00 Y500.00 Z20.00 E250.00              ; set accelerations (mm/s^2)
M906 X1200 Y1200 Z1200 E800 I30                  ; set motor currents (mA) and motor idle factor in per cent
M84 S30                                          ; Set idle timeout

; Axis Limits
M208 X-20 Y-20 Z0 S1                             ; set axis minima
M208 X305 Y295 Z200 S0                           ; set axis maxima

; Endstops
M574 X1 S1 P"121.io1.in"                         ; configure active-high endstop for low end on X via pin io0.in
M574 Y2 S1 P"io6.in"                             ; configure active-high endstop for low end on Y via pin io1.in



; Z-Probe
M950 S0 C"^121.io0.out"                          ; create servo pin 0 for BLTouch
M558 P9 C"^121.io0.in" H5 F120 T6000             ; set Z probe type to bltouch and the dive height + speeds
G31 P500 X0 Y70 Z0.55                            ; set Z probe trigger value, offset and trigger height
M557 X-12:293 Y70:315 P4                      	 ; define mesh grid

; Heaters
M308 S0 P"temp0" Y"thermistor" T100000 B4138     ; configure sensor 0 as thermistor on pin temp0
M950 H0 C"out0" T0                               ; create bed heater output on out0 and map it to sensor 0
M307 H0 R0.291 C1127.4 D26.90 S1.00				 ; Set PID for bed values
M140 H0                                          ; map heated bed to heater 0
M143 H0 S100                                     ; set temperature limit for heater 0 to 100C

M308 S1 P"121.temp0" Y"thermistor" T100000 B4725 ; configure sensor 1 as thermistor on pin 121.temp0
M950 H1 C"121.out0" T1                           ; create nozzle heater output on 121.out0 and map it to sensor 1
M307 H1 B0 R2.839 C310.4:158.7 D4.47 S1.00 V23.9  ; Set PID for hotend values
M143 H1 S280                                     ; set temperature limit for heater 1 to 280C

; Fans
M950 F0 C"121.out2" Q500                         ; create part cooling fan 0 on pin toolboard out1 and set its frequency
M106 P0 S0 H-1                                   ; set fan 0 value. Thermostatic control is turned off
M950 F1 C"121.out1" Q500                         ; create hotend fan 1 on pin toolboard out1 and set its frequency
M106 P1 S1 H1 T45                                ; set fan 1 value. Thermostatic control is turned on

; Tools
M563 P0 D0 H1 F0                                 ; define tool 0
G10 P0 X0 Y0 Z0                                  ; set tool 0 axis offsets
G10 P0 R0 S0                                     ; set initial tool 0 active and standby temperatures to 0C

; Custom settings are not defined

@jay_s_uk

you were too fast and replied before I removed my post!

I assumed the 'tool fan' was the hotend fan, but it isn't. If I take both of these down to 0, only the part cooling fan stops.
Although I'm not sure why there are two fans showing in the UI

deleted.
Thought it wasn't working but it is

@gloomyandy

Well I thought it was working, but I think there is still a slight issue with the duet config or slicer.

The hotend fan turns on correctly at 45C
But the part cooling fan doesn't start automatically. If I use the fan slider once the print has started it does work.
The slicer is set to enable it at layer two.

@gloomyandy

thanks for you r help with this. I removed the 1LC, reflowed the connectors with plenty of flux and cleaned with IPA - now working.

@gloomyandy

Yes definitely bridged to 3.3v (top two pins on the IO1 connector)

Here you go

; Configuration file for Duet WiFi (firmware version 3)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool v3.2.3 on Wed Jun 02 2021 18:38:31 GMT+0800 (中国标准时间)

; General preferences

G90                                              ; send absolute coordinates...
M83                                              ; ...but relative extruder moves
M550 P"BLV mgn Cube"                		     ; set printer name
M669 K1                                          ; select CoreXY mode

; Network
M552 S1                                          ; enable network
M586 P0 S1                                       ; enable HTTP
M586 P1 S0                                       ; disable FTP
M586 P2 S0                                       ; disable Telnet

G4 S1   										 ;wait for expansion boards to start

; Drives
M569 P0.0 S0 D2                                  ; X motor runs forwards
M569 P0.1 S1 D2                                  ; Y motor runs forwards
M569 P0.2 S1 D2                                  ; physical drive 0.2 goes backwards
M569 P0.3 S1 D2                                  ; physical drive 0.2 goes backwards
M569 P0.4 S1 D2                                  ; physical drive 0.2 goes backwards
M569 P121.0 S1 D2                                ; physical drive 121.0 goes backwards
M584 X0.0 Y0.1 Z0.2:0.3:0.4 E121.0               ; set drive mapping
M350 X16 Y16 Z16 E16 I1                          ; configure microstepping with interpolation
M92 X200.00 Y200.00 Z3200.00 E700                ; set steps per mm
M671 X0:290:290 Y155:62:255 S3 		 		     ; leadscrews at rear left, front middle and rear right
M566 X600.00 Y600.00 Z150.00 E3000.00            ; set maximum instantaneous speed changes (mm/min) - increased Z and E
M203 X20000.00 Y20000.00 Z2000.00 E6000.00       ; set maximum speeds (mm/min) - increased E
M201 X3000.00 Y3000.00 Z200.00 E5000.00          ; set accelerations (mm/s^2)
M906 X1600 Y1600 Z1000 E800 I30                  ; set motor currents (mA) and motor idle factor in per cent
M84 S30                                          ; Set idle timeout

; Axis Limits
M208 X-3:305 Y-50:305 Z-1.0:500.0 

; Endstops
M574 X1 S1 P"121.io1.in"                         ; configure active-high endstop for low end on X via pin io1.in
M574 Y2 S1 P"io6.in"                             ; configure active-high endstop for HIGH end on Y via pin io6.in
M564 H1											 ; allow jog without homing

; Z-Probe
M950 S0 C"^121.io0.out"                          ; create servo pin 0 for BLTouch
M558 P9 C"^121.io0.in" H3 F120 T10000            ; set Z probe type to bltouch and the dive height + speeds
G31 P500 X0 Y66 Z2.55                            ; set Z probe trigger value, offset and trigger height. + brings noxzzle closer to bed
M557 X5:305 Y20:290 P8                       	 ; define mesh grid

; Heaters
M308 S0 P"temp0" Y"thermistor" T100000 B3950     ; configure sensor 0 as thermistor on pin temp0
M950 H0 C"out0" T0                               ; create bed heater output on out0 and map it to sensor 0
M307 H0 R0.291 C1127.4 D26.90 S1.00				 ; Set PID for bed values
M140 H0                                          ; map heated bed to heater 0
M143 H0 S100                                     ; set temperature limit for heater 0 to 100C

M308 S1 P"121.temp0" Y"thermistor" T100000 B4725 C7.06e-8 	; configure sensor 1 as thermistor on pin 121.temp0 //0 to 1
M950 H1 C"121.out0" T1                           			; create nozzle heater output on 121.out0 and map it to sensor 1
M307 H1 B0 R3.089 C258.2:154.4 D5.95 S1.00 V23.7 			; Set PID for hotend values
M143 H1 S280                                     			; set temperature limit for heater 1 to 280C

; Fans
M950 F0 C"121.out2" Q80                          ; create hotend fan 0 on pin toolboard out1 and set its frequency
M106 P0 S0 H1 T45 C"Hotend Fan"                  ; set fan 0 value. Thermostatic control is turned on
M950 F1 C"121.out1" Q250                         ; create cooling fan 1 on pin toolboard out1 and set its frequency
M106 P1 S0 H-1 B1 C"Part Cooling Fan"            ; set fan 1 value. Thermostatic control is turned off

; Tools
M563 P0 D0 H1 F1   					 			 ; define tool 0
G10 P0 X0 Y0 Z0 								 ; set tool 0 axis offsets
G10 P0 R0 S0 									 ; set initial tool 0 active and standby temperatures to 0C
;
;M563 P1 D0 H1 F1 						  		 ; define tool 1
;G10 P1 X0 Y0 Z0 								 ; set tool 1 axis offsets
;G10 P1 R0 S0 									 ; set initial tool 1 active and standby temperatures to 0C

; Custom settings
M564 H0                                   	   	 ; Let the Jog buttons work blv: added to allow jog buttons
M575 P1 B57600 S1								 ; Connection to  PanelDue
;955 P121.0 I10									 ; Accelerometer 

; Pressure advance
;M572 D0 S0.04

; Miscellaneous
M911 S21 R22 P"M913 X0 Y0 G91 M83 G1 Z3 E-5 F1000" ; set voltage thresholds and actions to run on power loss

@gloomyandy It does! But the hotend temp drops to -271 and the thermostatic fan comes on.

@nick9one1

testing the endstop with a multimeter shows its closed when not pressed and open when pressed.

I've temporarily disconnected it and bridged IO1.in and GND with a screwdriver - no change on the X endstop.

@gloomyandy

thanks I found it. I can see the Y tool position change to green on activation.
For some reason X still doesn't work

Just double checking I'm correct to have it wired to IO1.in and GND? not IO1.in and 3.3v?

@gloomyandy

thanks, looks like we're on the same page. I just updated.

No errors anymore, but the X endstop still isn't detected by the endstop monitor..

I've just forced a firmware update with M997 B121

Now i dont get an error and it will attempt to home. But crashed into the endstop as it doesn't seem to be detecting it.
endstop plugin also isn't detecting when pressed.