We noticed that there was some twitching in some of the overlays. After observing and playing around it with it a bit, I found that the problem lied in transplanting everything above the root. Update: Ignoring the lower back joint and transplanting everything above it looks better but loses some of the movement of the motion.
I'm also keeping in mind other methods of alignment, namely spatial alignment mentioned in the paper "Splicing Upper-Body Actions with Locomotion" by Heck, Kovar, and Gleicher. This involves finding a local rotation of the pelvis that best aligns the shoulders and spine of the upper body motion with that of the lower body motion. The best rotation is computed using point clouds.
Update: Something like the method mentioned above seems like a good way to start.
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