Mark, congratulations on getting the job done! It is very unlikely that a neo got demagnetized unless the plating got damaged and the material corroded, but you would have noticed that since it is not pretty. My only suggestion would be to leave the magnet on the high E as is and use smaller diameter buttons on the rest, varying as needed to make it work out. You might not hit it right on the next try, but I bet it will get a lot better. K&J Magnetics has hundreds of different sizes of buttons, if you have not checked them.
Also, neo does come in a couple of grades. Is it possible you got one from the weaker grade and the rest are stronger? I kind of of doubt this, but you might be able to check it you have access to a gauss meter with a small probe.
Speaking of corrosion, I have noticed that guitar players are not good for neodymium magnets; they should be protected as yours seems to be since they are between two pieces of board. But it might not be a bad idea to wax pot it for long life as well.