UPDATE: V2 now with a bit more narrow feet and chamfers to fit into the V-slots with more ease. Feetwidth is also configurable now.
In IMHO the best "building an Ender 3"-video
Tom gives a great hint to get the gantry properly leveled: Use the metal part of the spool holder as a defined spacer on both sides.
Very easy and clever solution.
Unless - you have a dual Z-axis that tends to be off a bit from time to time or your gantry starts to hang to one side as tension is getting loose or wheels wear out. Spool holder is mounted so what can we use as a well defined and good fitting spacer? I had nothing at home so I designed and printed it!
Just print two pieces and put it on the 4040 extrusion under the gantry. Move the gantry down until it sets on both spacers. Now you can adjust the excentric nuts or in my case put in the timing belt for the dual Z-axis.
Make sure, the spacers sits flush on the 4040 extrusion. I had to file down the notch a bit on the spacers as the retractions had added a bit to their width. You may also alter the size in OpenSCAD. As usual, I added the sourcefile.
Enjoy and have fun!