Ender 3 v3 plus x/z gantry anomalies

[3verteD]

This issue came up after rooting the printer. I started to see inconsistent circles (circles that are not round). I also noticed that the x gantry "flexes" about the front fan axis when doing x and diagonal movements (see the attached image and video). My assumption lies within the printer configuration because some sections differ from the factory printer configuration, particularly the driver sections. In the code below, you may note that the rotation distances differ from the factory, and some lines are commented out. If someone can assist me in fixing the circular movements and the gantry rotation I would greatly appreciate it. I have adjusted the belt tensions and done the relevant calibrations, but the anomaly is still present. I also attempted disabling gcode_arcs, with no luck. Going back to the factory firmware seems to have fixed the issues.

Rooted printer.cfg:
[stepper_x]
step_pin:PC2
dir_pin:PB9
enable_pin:!PC3
microsteps:32
rotation_distance: 72
/# endstop_pin:tmc2209_stepper_x:virtual_endstop
endstop_pin:PA5
position_endstop:-2
position_min:-4
position_max:304
homing_speed:60
homing_retract_dist:0#10
/# full_steps_per_rotation: 200
/# homing_positive_dir: true

[tmc2209 stepper_x]
uart_pin:PA9
driver_SGTHRS: 90
uart_address:3
interpolate: true
run_current:1.5
sense_resistor: 0.10
stealthchop_threshold: 0
diag_pin: ^PB12
driver_TBL: 0
driver_TOFF: 1
driver_HEND: 12
driver_HSTRT: 7

[stepper_y1]
step_pin: PB8
dir_pin: PB7
enable_pin: !PC3
microsteps: 32
rotation_distance: 32
endstop_pin: tmc2209_stepper_y:virtual_endstop

[tmc2209 stepper_y1]
uart_pin:PA10
driver_SGTHRS: 90
uart_address:3
interpolate: false
run_current:1.5
/# hold_current:0.5
sense_resistor: 0.10
stealthchop_threshold: 0
diag_pin: ^PB15
driver_TBL: 1
driver_TOFF: 2
driver_HEND: 2
driver_HSTRT: 4

[stepper_y]
step_pin: PB4
dir_pin: PB3
enable_pin: !PC3
microsteps: 32
rotation_distance: 32
/# endstop_pin: !PA12
endstop_pin: tmc2209_stepper_y:virtual_endstop
position_endstop: -3
position_min: -3
position_max: 305
homing_speed: 30
homing_retract_dist:0

[tmc2209 stepper_y]
uart_pin:PA12
driver_SGTHRS: 90
uart_address:3
interpolate: false
run_current:1.5
/# hold_current:0.5
sense_resistor: 0.10
stealthchop_threshold: 0
diag_pin: ^PB15
driver_TBL: 1
driver_TOFF: 2
driver_HEND: 2
driver_HSTRT: 4

Factory printer.cfg:
[stepper_x]
step_pin: PC2
dir_pin: !PB9
enable_pin: !PC3
microsteps: 32
rotation_distance: 72
endstop_pin: tmc2209_stepper_x:virtual_endstop
position_endstop: 306.5
position_min: -2
position_max: 306.5
homing_speed: 36
homing_retract_dist:0

[tmc2209 stepper_x]
uart_pin:PA9
interpolate: True
run_current:1.5
hold_current:1.0
sense_resistor: 0.100
stealthchop_threshold: 0
uart_address:3
diag_pin: ^PB12
/# driver_IHOLDDELAY: 8
/# driver_TPOWERDOWN: 20
/# driver_TBL: 1
/# driver_TOFF: 1
/# driver_HEND: 0
/# driver_HSTRT: 7
driver_SGTHRS: 65

[stepper_y]
step_pin: PB8
dir_pin: !PB7
enable_pin: !PC3
microsteps: 32
rotation_distance: 72
endstop_pin: tmc2209_stepper_y:virtual_endstop
position_endstop: -2
position_min: -2
position_max: 306
homing_speed: 36
homing_retract_dist:0

[tmc2209 stepper_y]
uart_pin:PA10
interpolate: True
run_current:1.5
hold_current:1.0
sense_resistor: 0.100
stealthchop_threshold: 0
uart_address:3
diag_pin: ^PB13
/# driver_IHOLDDELAY: 8
/# driver_TPOWERDOWN: 20
/# driver_TBL: 1
/# driver_TOFF: 1
/# driver_HEND: 0
/# driver_HSTRT: 7
driver_SGTHRS: 65

WhatsApp.Video.2024-10-28.at.14.33.09.mp4