You can use 3drefit to change one dataset's grid to match another's, but this doesn't change the data itself. That is, if the datasets overlap properly when viewed in AFNI as they are before the change, then they won't overlap properly after the change. This is because AFNI's viewer overlays datasets based on xyz coordinates, whereas all other programs that combine multiple datasets do so on a voxel-wise basis. So you have to be careful when you are changing the mapping between voxel ijk indexes and xyz coordinates!

3drefit -duporigin seems like the option you want, if your datasets are properly aligned in ijk indexes and not properly aligned in xyz coordinates.