I'm not clear as to what you're trying to do. With the tagset plugin, you would set your points in the exact same order for two datasets. Then use 3dTagalign to affinely align one dataset to the other. The affine transformation is computed and stored in the header of the dataset. You could use the Nudge plugin afterwards too. cat_matvec can concatenate the two transformations together. You may then apply the transformation with 3dAllineate or 3drotate. Directions of the transformation matrices are important here, so you have to be consistent, and you may need to take the inverse of each.
