Before i switched to Duet 3D WiFi i use to get virtually flawless prints. I have the same hardware setup (ex CR-!0s).
No changes have been made to the hardware except the X and Y stepper motors (STEPPERONLINE Nema 17 Bipolar Stepper 0.9deg(400 steps/rev) 1.68A 44Ncm(62.3oz.in) Motor).
The Z axis are still the stock motors (CR-10 Series NEMA17/34 Motor JK42HS34-0844YA-06F 1.8deg)

Since then i get these horizontal lines on X and Y axis, some uniform spaced and some not.
I was thinking if the settings in M350 for Z are not correct as it being different in stepper degrees.
Would replacing the CR-10 1.8deg steppers for 0.9deg steppers solve this issue?
I have checked the Z motor shafts, couplings and lead screws for anomalies. They have no issues.

Thanks in advance.

Config.g setting

; Configuration file for Duet WiFi (firmware version 1.21)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool v2 on Mon Apr 01 2019 13:32:45 GMT-0500 (Central Daylight Time)

; General preferences
G90 ; Send absolute coordinates...
M83 ; ...but relative extruder moves

; Network
M550 P"xxxxxxxxx" ; Set machine name
M551 P"xxxxxxxxx" ; Set password
M552 S1 ; Enable network
M587 S"xxxxxxxxx" P"xxxxxxxxx" ; Configure access point. You can delete this line once connected
M586 P0 S1 ; Enable HTTP
M586 P1 S0 ; Disable FTP
M586 P2 S0 ; Disable Telnet

; Drives
M569 P0 S1 ; Drive 0 goes forwards
M569 P1 S1 ; Drive 1 goes forwards
M569 P2 S1 ; Drive 2 goes forwards
M569 P3 S0 ; Drive 3 goes backwards
M350 X16 Y16 Z16 E16 I1 ; Configure microstepping with interpolation
M92 X160.00 Y160.00 Z400.00 E836.00 ; Set steps per mm
M566 X400.00 Y400.00 Z24.00 E120.00 ; Set maximum instantaneous speed changes (mm/min)
M203 X30000.00 Y30000.00 Z900.00 E3000.00 ; Set maximum speeds (mm/min)
M201 X1000.00 Y1000.00 Z100.00 E250.00 ; Set accelerations (mm/s^2)
M906 X1200.00 Y1200.00 Z700.00 E700.00 I30 ; 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 X300 Y300 Z400 S0 ; Set axis maxima

; Endstops
M574 X1 Y1 S0 ; Set active low and disabled endstops

; Z-Probe
M574 Z1 S2 ; Set endstops controlled by probe
M307 H3 A-1 C-1 D-1 ; Disable heater on PWM channel for BLTouch
M558 P9 H2.5 F120 T6000 ; Set Z probe type to bltouch and the dive height + speeds
G31 P500 X5 Y26.5 Z1.27 ; Set Z probe trigger value, offset and trigger height
M557 X5:300 Y5:300 S30 ; Define mesh grid

; Heaters
M305 P0 T100000 B4138 R4700 ; Set thermistor + ADC parameters for heater 0
M143 H0 S120 ; Set temperature limit for heater 0 to 120C
M305 P1 B4725 C7.060000e-8 ; Set thermistor + ADC parameters for heater 1
M143 H1 S280 ; Set temperature limit for heater 1 to 280C

; Fans
M106 P0 S0 I0 F500 H-1 ; Set fan 0 value, PWM signal inversion and frequency. Thermostatic control is turned off
M106 P1 S1 I0 F500 H1 T45 ; Set fan 1 value, PWM signal inversion and frequency. Thermostatic control is turned on

; Tools
M563 P0 D0 H1 ; 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

; Automatic saving after power loss is not enabled

; Custom settings are not configured

Everything is calibrated, extrusion flow rate etc.

Its been a long time since i last used the reprap configuration tool and was wondering if its possible to export my existing firmware setup in the Duet3dWifi back to the reprap configuration tool (JSON template) without having to start from the beginning?
The only mod i have made with the printer is a new print head. (Mosquito). Will that require any changes in the thermistor setup? Thanks.

Totally out of my range!, Think i'll stick to the install i have now. Thanks for the reply!

Does this Release 3.0 requires no further action when i upload zip file to /sys and /www Directories??
Below is my current version.

Firmware Name: RepRapFirmware for Duet 2 WiFi/Ethernet
Firmware Electronics: Duet WiFi 1.02 or later
Firmware Version: 2.03 (2019-06-13b2)
WiFi Server Version: 1.23
Web Interface Version: 1.22.6

Thanks.

@phaedrux The lines are there just hard to focus at macro level and the poor light. They are random and some evenly spaced which made me think it could me the lead screw or connectors not plum.
They're in sync. I have traveled the Z axis to max and back to min and then used a 3" x 1" calibrated metal block to check if the X axis is level with the bed, which it is.

@dc42 I did upgrade to dual axis and that came with like a "2 in 1" cable connection. So using that might solve the issue?

Everything is calibrated, extrusion flow rate etc.

Before i switched to Duet 3D WiFi i use to get virtually flawless prints. I have the same hardware setup (ex CR-!0s).
No changes have been made to the hardware except the X and Y stepper motors (STEPPERONLINE Nema 17 Bipolar Stepper 0.9deg(400 steps/rev) 1.68A 44Ncm(62.3oz.in) Motor).
The Z axis are still the stock motors (CR-10 Series NEMA17/34 Motor JK42HS34-0844YA-06F 1.8deg)

Since then i get these horizontal lines on X and Y axis, some uniform spaced and some not.
I was thinking if the settings in M350 for Z are not correct as it being different in stepper degrees.
Would replacing the CR-10 1.8deg steppers for 0.9deg steppers solve this issue?
I have checked the Z motor shafts, couplings and lead screws for anomalies. They have no issues.

Thanks in advance.

Config.g setting

; Configuration file for Duet WiFi (firmware version 1.21)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool v2 on Mon Apr 01 2019 13:32:45 GMT-0500 (Central Daylight Time)

; General preferences
G90 ; Send absolute coordinates...
M83 ; ...but relative extruder moves

; Network
M550 P"xxxxxxxxx" ; Set machine name
M551 P"xxxxxxxxx" ; Set password
M552 S1 ; Enable network
M587 S"xxxxxxxxx" P"xxxxxxxxx" ; Configure access point. You can delete this line once connected
M586 P0 S1 ; Enable HTTP
M586 P1 S0 ; Disable FTP
M586 P2 S0 ; Disable Telnet

; Drives
M569 P0 S1 ; Drive 0 goes forwards
M569 P1 S1 ; Drive 1 goes forwards
M569 P2 S1 ; Drive 2 goes forwards
M569 P3 S0 ; Drive 3 goes backwards
M350 X16 Y16 Z16 E16 I1 ; Configure microstepping with interpolation
M92 X160.00 Y160.00 Z400.00 E836.00 ; Set steps per mm
M566 X400.00 Y400.00 Z24.00 E120.00 ; Set maximum instantaneous speed changes (mm/min)
M203 X30000.00 Y30000.00 Z900.00 E3000.00 ; Set maximum speeds (mm/min)
M201 X1000.00 Y1000.00 Z100.00 E250.00 ; Set accelerations (mm/s^2)
M906 X1200.00 Y1200.00 Z700.00 E700.00 I30 ; 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 X300 Y300 Z400 S0 ; Set axis maxima

; Endstops
M574 X1 Y1 S0 ; Set active low and disabled endstops

; Z-Probe
M574 Z1 S2 ; Set endstops controlled by probe
M307 H3 A-1 C-1 D-1 ; Disable heater on PWM channel for BLTouch
M558 P9 H2.5 F120 T6000 ; Set Z probe type to bltouch and the dive height + speeds
G31 P500 X5 Y26.5 Z1.27 ; Set Z probe trigger value, offset and trigger height
M557 X5:300 Y5:300 S30 ; Define mesh grid

; Heaters
M305 P0 T100000 B4138 R4700 ; Set thermistor + ADC parameters for heater 0
M143 H0 S120 ; Set temperature limit for heater 0 to 120C
M305 P1 B4725 C7.060000e-8 ; Set thermistor + ADC parameters for heater 1
M143 H1 S280 ; Set temperature limit for heater 1 to 280C

; Fans
M106 P0 S0 I0 F500 H-1 ; Set fan 0 value, PWM signal inversion and frequency. Thermostatic control is turned off
M106 P1 S1 I0 F500 H1 T45 ; Set fan 1 value, PWM signal inversion and frequency. Thermostatic control is turned on

; Tools
M563 P0 D0 H1 ; 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

; Automatic saving after power loss is not enabled

; Custom settings are not configured

My old Marlin printer used the following clean nozzle start script from S3D:

G21 ; (metric values)
G90 ; (absolute positioning)
M82 ; (set extruder to absolute mode)
M203 E80 ; (set extruder max to 80)
G28 ; (home all axis)
G29 ; (Auto Level)
G92 E0 ; (reset extruder)
G1 Z1.0 F3000 ; (move z up little to prevent scratching of surface)
G1 X0.1 Y20 Z0.2 F5000.0 ; (move to start-line position)
G1 X0.1 Y200.0 Z0.2 F1500.0 E15 ; (draw 1st line)
G1 X0.4 Y200.0 Z0.2 F5000.0 ; (move to side a little)
G1 X0.4 Y20 Z0.2 F1500.0 E30 ; (draw 2nd line)
; G1 E27 F1000 ; (retract filament 1mm)
G92 E0 ; (reset extruder)
G1 Z1.0 F3000 ; (move z up little to prevent scratching of surface)

My S3D script i use at the moment with the Duet is:

G28 XY ;Home XY
M561 ; Clear any bed transform that might be in place
G1 X150.5 Y150 ; Move BLTouch Probe to middle of bed
G30 ; Do a single probe
M375 ; Load Height Map
G1 Z20.0 F6000 ; Move Z to 20
M82 ; set absolute extruder mode

.. which is fine, but its getting a pain having to quickly clear away the melted plastic off the print surface as it misses out doing the clean nozzle routine.
It use to print 2 parallel lines, then the nozzle while at the correct print gap forced out extra plastic, lifted up quick then moved to the print start
What would go where from the old start script, cause when it comes to G Code i'm lost!
Heat bed size 280x280mm.
Thanks!

Thanks, Worry over!

I think i saw somewhere that on the newer Duet3D WiFi 1.04 boards you don't need to cut the copper line logic conversion on the BLTouch Smart. Is there any truth to this?