Looks quite good now. The config blocks for your TMC2209 are missing. Add:
[tmc2209 stepper_x]
uart_pin: PD5
interpolate: false
sense_resistor: 0.110
run_current: .8
[tmc2209 stepper_y]
uart_pin: PD7
interpolate: false
sense_resistor: 0.110
run_current: .8
[tmc2209 stepper_z]
uart_pin: PD4
interpolate: false
sense_resistor: 0.110
run_current: .8
[tmc2209 extruder]
uart_pin: PD8
interpolate: false
sense_resistor: 0.110
run_current: .8
Note the run_current. This needs to be set according to the stepper motors you are using. Refer to Hold_current and run_current -- TMC2209 - #5 by Sineos for some additional information
From your current config:
[stepper_x]
step_pin = PE3
dir_pin = !PE2
enable_pin = !PE4
I’d be surprised if the enable_pin required to be inverted (!).
Inverting dir_pin is possible depending on your stepper wiring. Use this to make sure the steppers turn the right direction