My warped holes are driving me insane

[curious aardvark]

Sounds like your steps might not be right, or belts might be looses or pulleys might not be even. I mean it's an ender 3 - it's a piece of junk, you're going to have problems.

If you print a 20x10x3 mm oblong at 0.3mm layer height, what actual dimensions do you get ?
stl attached :-)

Also fan speed should either be 100% or none. There's not really any point pissing about with inbetween speeds. For PLA the first layer you want it off, so it sticks better: for all other layers you want it blowing as hard as it can. The quicker you cool the plastic the more accurate the print will be.

What surface are you printing on ?