The magnets used are 6mm diameter by 3mm thick. The spacing is 20mm center to center. Don't forget to get the polarity of each magnet correct. There is only 0.1mm of clearance in the design for the magnets. They slipped in perfectly for me and then curing the print seems to be holding them into place.

07-11-19: adding a alternative stir "bar" I modeled up when I thought about going a different direction for a project.