The two sides of the magnetic yoke (the laminated steel part of the ignition module) should be the same distance from the magnet on the flywheel, and the distance should be about 0.012". Having said that, Honda specifies 0.016" plus or minus 0.008", so obviously they aren't all that fussy. Nevertheless the ends of the yoke need to be parallel to the surface of the flywheel. It sounds as if you may need to file the screw holes in the yoke just slightly with a needle file, to create some clearance. Warning: do not try to put a drill bit through those holes, or you will de-laminate the yoke, which will ruin the module.
