This is the method I’ve used for aligning flat burrs, and the best one that I’ve seen. I’m not going to claim a lot of experience with aligning burrs in coffee grinders, but I do have a lot of experience setting up alignments for woodworking machines, and a lot of the principles are the same.
The key tips from this method is to do alignment one burr at a time, and to spread out the shim placement should you need to place shims.
The reason to do one burr at a time is that assuming that the bottom burr is the one that rotates, checking the bottom burr first ensures that the flat grinding surface is perpendicular to the axis of rotation, and then you can align the top burr so that its grinding surfaces are parallel to the bottom burr. Trying to do both at once is a setup for frustration.