I’m not familiar with the Ender 3 Pro and the parts used within it but when I look at the klippy.log, I don’t see anything that unusual. The X/Y/Z steppers are all set to what I would think is a conservative 0.6A:
[tmc2209 stepper_x]
uart_pin = PB12
run_current = 0.600
stealthchop_threshold = 999999
The first thing I would suggest you try is to reduce the current to 0.4A and see if that resolves your issue.
How thick (what is the depth) of these steppers? That determines their size and the amount of current they can handle.