I have rerigged it with vertex groups… I did not include the base though because its wrong that it should turn with the root bone. I love the idea of vertex groups, it feels much cleaner to keep everything within the same object and simply group up vertices.
However, did anyone find that the bones seems to be slightly behind the geometry when moving them around now… they sometimes seem to go out of sync as well, I have to reset with Alt-r to fix it sometimes.
After rerigging I was lucky that the animation works completely as before and so does the inverse kinematics.
