You didn't mention where you were when you introduced the rhythmic movements.
The first floor looks to have enough bracing but I notice there isn't any knee bracing where the first floor meets the second floor, this could be a movement issue.
I also see you have large rectangles formed by your styles and girts, you might try changing that geometry into triangles to see if that stiffens up the framework enough so you wouldn't need to add knee bracing at the first floor/ second floor junction.
Any frame, regardless of construction type, is going to have some movement until it is all buttoned up. This is partly a function of the added weight, weight is stabilizing since it travels down.
If you put the full roof on, that weight will travel down through the posts or at least it is supposed to.
Triangles are stiff in all directions, their shape takes loading from one post to the next and so stiffens the superstructure.
Rectangles are able to wobble on the long sides since there really isn't any loading of that portion of the superstructure, that is one reason geodesic domes are so stiff, every section is diagonally braced
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