Edit: I have moved away from a printed part to go between the screw and stepper, I have now gone to a 1/4" ball bearing. See additional pictures above that illustrate the possible situations.

Having alignment issues on your Ender 3 Pro beyond just needing the Z stepper spacers? Well I was and Im sure Im not the only one. I wanted to install the anti-backlash nut and I could not due to my Z axis bracket on the Gantry is not all perfect. The anit-Backlash nut is fairly high precison compared to the sloppy stock nut.

So I bought these spiral cut flexible couplerss from Amazon:
https://www.amazon.com/gp/product/B081SK9R64/

Then I noticed the next problem... If both end shafts are cut square and touch inside the coupler, it will in effect make a solid column clamped together with the coupler. So next step, add space, then next problem- compression. The weight of the Z Axis is not enough to fully compress the coupler, but any weight is adding to a bind.

So heres the fix package. Early on with this printer I came up with a bearing shield to keep gunk out of the Z Axis stepper bearing. I have included the file here as its part of the stack up. Next is the coupler spacer. EDIT: the printed part proved to not last, so it has been replaced with a single 1/4" diameter ball bearing. The 1/4" size fits well into the coupler, stays fairly well centered.

This will alleviate the pressure off the coupler and allow flex without making a solid column situation. My Z Axis is now snug and accurate with NO slop.

Happy Printing!