If the two rare earth magnets came together the way they are mounted, would they repel each other or attract? They should attract. That is their polarity should all face the same direction.
It really doesn't take much to magnetize an alnico using rare earth magnets. When passing them through it is best to not let the alnico touch the rare earth magnets. Try insulating the charging magnets with a very thin piece of cardboard, like you find on the back of a legal pad. Pass the pickup through at a steady rate and try to keep an even path and stay on path until well away from the charging magnets.
Once charged be sure to keep them away from anything that may take the charge away. Any pics of your setup?