I just want to state that I ordered right after you and brought both issues, missing balls and machining, to his attention and he assured me that they now check to make sure all the balls are there. Also, my nut looks like it was milled down on both sides and it has no appreciable backlash when moving by hand. I cannot comment on the change of threads because I got the bdtools mounts and they just specified a "12mm dia thread" at that location. I will update this post with some pictures of my machined x-axis ballnut.
That is unfortunate you had such a bad experience with him though.